Health Discussion HSCI 410

I uploaded the book too

There are two parts to this module.
YOU WILL NEED TO ADDRESS BOTH QUESTIONS THIS MODULE with an initial post for each.
A total of 2 response posts is required for this module.

Module 5 part 1:

In this session, we describe rights and responsibilities for employees in the medical fields.

You are welcome to add another source, but feel free to use just the Atlantic article and Pozgar.
Readings:

Atlantic Monthly article on new models for treating employees:
http://www.theatlantic.com/business/archive/2014/11/a-new-business-strategy-treating-employees-well/383192/

Pozgar: Chapter 11–employment issues

 

Question 1:
Use your text and one other reference for your initial post.

For the first half of this semester we have been dealing with some very difficult issues. In employment, there are some ethical dilemmas we as health care workers may have to address as employees.

With this question I am putting a positive spin on this issue.
-Tell the class of one positive handling of employee rights and responsibilities by your current or recent employer.
-Then, explore one or two things you would look for in a new employment situation.

And, remember, as you move into management roles, you have an increasing say in improving employee environments!

Module 5 Part 2:

Question 2:
You have two choices for this question to focus on for your initial posting.

First, Look at these documents about consent:
This first is the National Institutes of Health’s patient information page on patients rights and links for them to explore what informed consent involves.

http://www.nlm.nih.gov/medlineplus/patientrights.html

The second is the Illinois Medical Patient Rights Act

http://www.ilga.gov/legislation/ilcs/ilcs3.asp?ActID=1525&ChapterID=35

Now, watch the short video from Consumer Reports on security issues with personal devices.

http://www.consumerreports.org/cro/magazine/2015/06/connected-devices-and-your-privacy/index.htm

And read this Washington post article about employers collecting FIT BIT data:

https://www.washingtonpost.com/business/economy/with-fitness-trackers-in-the-workplace-bosses-can-monitor-your-every-step–and-possibly-more/2019/02/15/75ee0848-2a45-11e9-b011-d8500644dc98_story.html?utm_term=.611ff15b76aa

Then, select ONE of the following for your initial posting. Use our text AND one of the links above as references for your post.

Choice 1:
Take an example from another profession (ex. criminal justice, psychology, nutrition, etc.) where a citizen/patient/client refuses to accept a recommendation that would benefit them. How would you respond, in your role as a police officer, psychologist, nutritionist, etc., knowing that a refusal could likely harm the individual? Should you challenge the refusal? (You should take into account the basic concepts of ethics AND the profession’s code of ethics, practice law, state regulations).

Choice 2:
Identify and examine the issues of informed consent in our on-line culture. We click “Accept” to lines and lines of legal language for every app we use.
Does your electronic FITBIT gather data on your health and activities?
Does your server log how often you search health care sites?
With whom does the company share this data?
Will this lead to employers knowing about our activities?
Does the concept of informed consent become muddied by the legal and technical language in our check boxes?
If you select this choice I encourage you to include a few lines of the consent language from the chosen technology.

THIRD EDITION

 

 

Legal and Ethical Issues

for Health Professionals

George D. Pozgar, MBA, CHE

Consultant

GP Health Care Consulting

Annapolis, Maryland

Legal Review

Nina Santucci, JD

Medical Review

John W. Pinnella, MD, DDS, FICS

 

 

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To order this product, use ISBN: 978-1-4496-7211-9

Library of Congress Cataloging-in-Publication Data

Pozgar, George D.

 

 

Legal and ethical issues for health professionals / George D. Pozgar. — 3rd ed. p. cm.

Includes bibliographical references and index.

ISBN 978-1-4496-4775-9

I. Title.

[DNLM: 1. Ethics—United States. 2. Legislation, Medical—United States. 3. Ethics, Clinical— United States. 4. Patient Rights—United States. W 32.5 AA1]

KF3821.P68 2010

174.2—dc23 2011051293

6048

Printed in the United States of America

16 15 14 13 12 10 9 8 7 6 5 4 3 2 1

 

 

What lies behind us and what lies before us are tiny matters

compared to what lies within us.

Henry S. Haskins

 

 

Contents

Foreword

Preface

Acknowledgments

Chapter One Introduction to Ethics

Introduction

Ethics

Morality

Ethical Theories

Principles of Ethics

Virtue Ethics and Values

Religious Ethics

Secular Ethics

Atheism

Situational Ethics

The Final Analysis

The Moral Compass

Summary Thought

Chapter Review

Test Your Understanding

Chapter Two Contemporary Ethical Dilemmas

Introduction

Noteworthy Historical Events

Abortion

Acquired Immune Deficiency Syndrome

Artificial Insemination

Organ Donations

 

 

Research, Experimentation, and Clinical Trials

Sterilization

Wrongful Birth, Life, and Conception

Surrogacy

Human Genetics

Chapter Review

Test Your Understanding

Notes

Chapter Three End-of-Life Dilemmas

Introduction

Euthanasia

Advance Directives

Futility of Treatment

Withdrawal of Treatment

Do-Not-Resuscitate Orders

Chapter Review

Test Your Understanding

Notes

Chapter Four Health Care Ethics Committee

Introduction

Committee Structure

Goals of the Ethics Committee

Committee Functions

Requests for Consultations

Expanding Role of the Ethics Committee

Convening the Ethics Committee

Reasoning and Decision Making

Helpful Hints

Chapter Review

Test Your Understanding

Notes

Chapter Five Development of Law

 

 

Introduction

Sources of Law

Government Organization

Administrative Departments and Agencies

Chapter Review

Test Your Understanding

Notes

Chapter Six Introduction to Law

Introduction

Tort Law

Negligence

Intentional Torts

Criminal Law

Contracts

Trial Procedures and the Courtroom

Chapter Review

Test Your Understanding

Notes

Chapter Seven Government, Ethics, and the Law

Introduction

United States Office of Government Ethics

Public Policy as a Principle of Law

14 th

Amendment to the U.S. Constitution (1868)

Civil Rights Act (1964)

Sherman Antitrust Act (1890)

Privacy Act (1974)

Health Insurance Portability and Accountability Act (1996)

Emergency Medical Treatment and Active Labor Act (1986)

Health Care Quality Improvement Act (1986)

Agency for Healthcare Research And Quality

Ethics in Patient Referral Act (1989)

Patient Self-Determination Act (1990)

Sarbanes-Oxley Act (2002)

 

 

Patient Protection and Affordable Care Act (2010)

Political Malpractice

Ethics in Public Service

Chapter Review

Test Your Understanding

Notes

Chapter Eight Organizational Ethics and the Law

Introduction

Code of Ethics for Organizations

Organizational Conduct Under Scrutiny

Doctrine of Respondeat Superior

Corporate Negligence

Corporate Duties and Responsibilities

Avoid Conflicts of Interest

Provide for Effective Communications

Chapter Review

Test Your Understanding

Notes

Chapter Nine Health Care Professionals’ Ethical and Legal Issues Introduction

Chiropractor

Dentist

Dental Hygienist

Dieticians

Emergency Department Staff

Emergency Medical Technician

Medical Technologist

Medical Assistant

Medical Records

Nurse

Pharmacist

Physical Therapist

Physician Assistant

 

 

Psychologist

Respiratory Therapist

Radiology Technologist

Social Worker

Certification of Health Care Professionals

Licensing Health Care Professionals

Helpful Advice for Caregivers

Chapter Review

Notes

Chapter Ten Physicians’ Ethical and Legal Issues Introduction

Principles of Medical Ethics

Credentialing Professionals

Hospital’s Duty to Ensure Competency Honoring a Patient’s Right to Autonomy Failure to Provide Informed Consent

Abandonment

Aggravation of a Preexisting Condition

Alternative Procedures: Two Schools of Thought

Confidential Communications

Falsification of Records

Failure to Respond: Emergency Department Call

Failure to Read Nurses’ Notes Failure to Refer for Consultation

Failure to Obtain Adequate History and Physical

Infection Control Issues

Medications

Misdiagnosis

Obstetrics and Gynecology

Physician–Patient Relationship Chapter Review

Notes

Chapter Eleven Employee Rights and Responsibilities

 

 

Introduction

Employee Rights

Employee Responsibilities

Helpful Advice

The Caregiver’s Pledge Chapter Review

Notes

Chapter Twelve Patient Consent

Introduction

Informed Consent

Consent and Ethical Codes

Assessing Decision-Making Capacity

Adequacy of Consent

Proof of Consent

Who May Authorize Consent?

Implied Consent

Right to Refuse Treatment

Statutory Consent

Chapter Review

Test Your Understanding

Notes

Chapter Thirteen Patient Abuse

Introduction

Child Abuse

Senior Abuse

Look Closer, See ME

Chapter Review

Notes

Chapter Fourteen Patient Rights and Responsibilities

Introduction

Patient Rights

Patient Responsibilities

 

 

Chapter Review

Notes

Chapter Fifteen Summary Case—Star Chamber Characters

Settings

Events of Sunday, October 2

Events of Wednesday Afternoon, October 5

Events of Thursday Morning, October 6

Events of Thursday Luncheon, October 6

Events of Thursday, Late Afternoon, October 6

Events of Thursday Evening, October 6

Events of December 27–29 Educational Conference Discussion

Note

Appendix A Pillars of Moral Strength

Appendix B Websites

Ethics Websites

Government and Government-Related Websites

Legal Websites

Best Practices Websites

Health Care Resources

Hospital and Physician Finders

International Medical Websites

Reference Websites

Glossary

Index

 

 

Foreword

Health care is personal. It is perhaps the most personal of any service any

of us will receive in our lifetime. We all need it and recognize its

importance. And we need to know that our health care delivery system has

ethical and legal integrity as well as scientific validity. Sometimes correct

choices are not always obvious. There are gray areas. That is why health

care administrators and providers need a resource such as this book to help

clarify their responsibilities and to help guide them through the tough

choices that inevitably occur. Intuition and good intentions are laudable but

are not enough when it comes to health care. There are specific criteria that

our society requires in this very sensitive area. Awareness of those criteria

is crucial. That information, however, comes from a variety of sources that

are not always readily accessible. This book concentrates much of that

information into one convenient volume. It provides the reader with the

proper foundation to make good decisions in the delivery of patient care.

That is the ultimate goal of this book.

John W. Pinnella, MD, DDS, FICS

 

 

Preface

How far you go in life depends on your being tender with the young,

compassionate with the aged, sympathetic with the striving, and tolerant

of the weak and strong. Because someday in life you will have been all

of these.

GEORGE WASHINGTON CARVER

Legal and Ethical Issues for Health Professionals, Third Edition provides

the reader with a clear understanding of the law and ethics as they relate to

health care dilemmas. The practical application of ethics in the health care

setting is accomplished by interspersing the thoughts of great minds

through Quotes, events in the world through Newspaper Clippings,

provider and organizational experiences through Reality Checks, patient

experiences through People Stories, and legal rulings and summaries

through Cases. The book ends with a closet drama that illustrates the real

world of human behavior and ties together the elements of the book in one

case.

The reader is presented in the Third Edition with real-world life

experiences that bring the reader through a journey of learning that

provides an effective transitional stage from the classroom to the reality of

the everyday work environment.

This book is a comprehensive reference dealing with the questions of

right and wrong. The reader will learn how to evaluate and distinguish

between the rightness and wrongness of alternative courses of action when

faced with complicated ethical problems. Ethics in the health care setting

are about doing the right thing for both patients and caregivers. It involves

recognizing ethical dilemmas and effectively addressing them. This book

provides the reader with:

• Basic principles of ethics and the law in an easily understood format.

 

 

• Insight into how ethics and the law are intertwined. • Features such as Newspaper Clippings, Reality Checks, People Stories,

and Cases to illustrate real-life issues.

• The tools to help guide the reader to additional resources in the study of ethics and the law.

• An understanding of how ethics and the law assist the reader in resolving ethical conflicts and dilemmas.

• A better understanding of the application of ethical principles and values in the health care setting.

• A clearer understanding of the rights of patients and caregivers.

When people consider matters of ethics they are usually considering

matters of freedom in regard to personal choices, one’s obligations to other sentient beings, or judgments about human character and the right to

choose.

This book, as with the first and second editions, starts with the premise

that to act in an ethical manner means to engage in conduct according to

accepted principles of right and wrong. The author’s objective is to provide the reader with the background knowledge necessary to understand that

ethical behavior begins with understanding that we have alternatives and

choices in our behavior regarding how we treat ourselves and how we treat

others. To make good decisions, we must first understand that they will be

only as good as our knowledge of what is “right” and what is “wrong.” Thus, it is important to study ethics and apply the principles learned when

addressing common health care dilemmas.

This book is not an indictment of any profession or organization. It

does, however, illustrate how a minority of people can often cast a dark

shadow on all the good that occurs by so many for so many. It is about

learning how the system can break down and how we can so easily fix it

simply by good people doing good things. The book is a “call to arms” to do good things, to stand out from the crowd, because acts of caring,

compassion, and kindness often go unnoticed.

GP

 

 

A study titled “Does Ethics Education Influence the Moral Action of Practicing Nurses and Social Workers?” published in the American Journal of Bioethics in July 2008 showed that “Ethics education has a significant positive influence on moral confidence, moral action, and use of ethics

resources.”1 There is a deluge of ethical issues in every aspect of human existence.

Although cultural differences, politics, and religion influence who we are,

it is all of life’s experiences that affect who we become. If we are compassionate, for example, it is most likely because we have been

influenced by the compassionate.

The headlines presented here and noted throughout the book are but a

few of the many reminders of how governments, organizations, the media,

and people from all walks of life have somehow become desensitized,

ethically complacent, and unwilling to accept responsibility for

wrongdoing.

NEWSPAPER CLIPPINGS: Executive’s Medicare Scheme Had Lobbying Effort to Support It

HE FRANCHISED FRAUD WITH ADVOCACY GROUP

Prosecutors say he pushed for policies to aid sham clinics

Miami health-care executive Larry Duran orchestrated one of the

largest Medicare frauds in U.S. history, submitting more than $205

million in phony claims and landing a record-breaking 50-year prison

sentence for his crimes.

But another piece of the Duran’s scheme also caught the eye of prosecutors. They say he extended his fraud through his lobbying

efforts, all aimed at getting official Washington to make it easier for

mental health centers such as his to make money.

 

 

Patients often suffered from Alzheimer’s disease, dementia or other conditions unsuited for therapy and were frequently left to urinate or

defecate on themselves as they waited for treatment that never came,

testimony showed.

“The people that were there were just kept there and run through like cattle,” the judge in the case said.

Dan Eggen, The Washington Post, October 5, 2011

Trek of tears describes many horrible historic events, from broken treaties

with American Indians to an African Journey of horror, where people

would flee together as a village to escape the barbaric slaughter of men,

women, and children as the remainder of the world stood cowardly by

watching the death and starvation of hundreds of thousands of people.

Human atrocities committed by humans. Is it not time to stand up and be

counted upon to do what is right and leave all excuses behind for our

complacency towards the genocide that continues throughout the world?

GP

Even the news media, whom we depend upon to report the truth, has failed

to provide a balanced view of right and wrong and good and bad. Views are

often slanted by even the best of journalists. For instance, “In the Footsteps of bin Laden” is a two-hour televised documentary on the life of Osama bin Laden produced by CNN. The documentary portrays him as a glamorous

terrorist leader. With some creative editing, it could be used as a powerful

visual tool for recruiting terrorists. Today, the news media also:

• Describes the nation’s vulnerabilities to terrorists (infrastructure, ports, and food supply chain).

• Describes how easy it is to make a bomb as well as where to find more information about the subject.

• Reports and dramatizes the failures of medicine, not the successes.

Cases containing a multitude of legal and ethical issues are included

throughout the book. The reader will be asked a series of questions after

each case, requiring legal and ethical logic in order to answer them.

Caregivers who have a clear grasp of the ethical and legal concepts

 

 

discussed in this book will be better equipped to make health care decisions

that are ethically sound and legally correct. The following case is an

example of how legal and ethical principles can be intertwined.

CASE: PATIENT AUTONOMY

Several months after having stomach surgery (2002), Vicki Marsingill, in

Marsingill v. O’Malley, 58 P.3d 495, called her surgeon, Dr. O’Malley, complaining of abdominal pain and nausea. O’Malley advised Marsingill to go to the emergency room and offered to meet her there, but Marsingill

said she felt better and declined to go.

O’Malley left it up to Marsingill whether to seek emergency room treatment. O’Malley informed Marsingill that the doctors in the emergency room would probably take X-rays and insert a nasogastric tube to relieve

the pressure in her stomach. After hearing that she would likely need to

have a nasogastric tube inserted if she went to the emergency room,

Marsingill ended the call, telling O’Malley that she was feeling better. Later that night, Marsingill’s husband found her unconscious on the

bathroom floor. Paramedics rushed her to the hospital, where an

emergency operation later revealed that she had experienced an intestinal

blockage, but by then the obstruction had caused Marsingill to go into

shock. She suffered brain damage and partial paralysis.

Marsingill sued O’Malley, claiming that he lacked the skill and knowledge to advise her properly and that the information he gave her

over the telephone did not allow her to make an intelligent treatment

decision.

Section 8.08 of the AMA Code of Medical Ethics addresses the duty of

disclosure, providing, “The patient’s right of self-decision can be effectively exercised only if the patient possesses enough information to

enable an intelligent choice.” Marsingill’s experts maintained that O’Malley had violated Section 8.08 by failing to give her enough information to make an intelligent choice about whether to seek

emergency room treatment. O’Malley acknowledged that Section 8.08 applied to his conduct—that he did have an obligation to give Marsingill

 

 

enough information so that she could make an intelligent choice as to

whether she should go to the emergency room.

Marsingill’s proposed instruction by the judge to the jury would have required the jury to decide the sufficiency of O’Malley’s communications from the standpoint of a reasonable patient in Marsingill’s position. The trial court rejected the proposed “reasonable patient” instruction.

O’Malley acquiesced in Marsingill’s decision not to go to the emergency room. In the context of a preexisting patient–physician relationship involving postoperative care, a physician’s recommendation to do nothing in the face of threatening symptoms is the equivalent of a

treatment recommendation and should be accompanied by a duty of

disclosure.

A physician’s acquiescence in a patient’s decision not to seek treatment in the same circumstances should likewise be regarded as

equivalent to a treatment recommendation subject to the same duty.

The superior court deprived Marsingill of her right to have the jury

decide the issue directly from the standpoint of a reasonable patient, and

the case was remanded for a new trial on Marsingill’s claim for breach of the duty to provide sufficient information to allow her to make an

intelligent treatment choice.

The appellate court ruled that the jury should have been instructed to

use the reasonable patient standard to determine whether O’Malley gave Marsingill sufficient information about her condition and treatment

choices. On remand, the jury must be instructed to decide the claim from

the standpoint of a reasonable patient.

There will always be an endless number of “what-if” scenarios. In the end, this question remains: What should one do, knowing that whatever

decision is made there will always be some doubt as to whether the

decision made was the right one? Armed with the knowledge in this book,

the reader will be a more effective caregiver and better able to make

critical health care decisions. The reader will make better choices with

fewer doubts.

Ethical and Legal Issues

1. Does the decision involve the principle of autonomy? If so, in what

way?

 

 

2. Is this an issue of professional ethics?

3. How did the physician’s actions involve the principles of beneficence and nonmaleficence?

4. Considering a patient’s rights and responsibilities, what rights were violated, if any? What responsibilities, if any, did the patient not

assume?

5. Do you agree with the court’s decision that the jury should have been instructed to use the reasonable patient standard? Discuss your answer.

 

 

ABOUT THE BOOK LAYOUT

Legal and Ethical Issues for Health Professionals, Third Edition begins

with an introduction to ethics and progresses to contemporary ethical

dilemmas, as well as end-of-life issues and health care ethics committees.

There are chapters describing the development of law and an introduction

to those aspects of the law that may have an impact on the careers of health

care professionals. The book continues with a discussion of government

ethics and the law, organizational ethics and the law, and the ethical–legal issues that health care professionals face. The book goes on to describe

employee rights and responsibilities, patient consent, patient abuse, and

patient rights and responsibilities. There is a summary case written as a

closet drama, as well as an appendix of suggested websites that includes a

brief description of what can be found on each website to help the reader

conduct further research into the legal and ethical issues of health care. The

text also provides a glossary of ethics and legal terminology

Newspaper Clippings are dispersed throughout the book. Because many

high-profile cases are settled out of the courtroom due to the negative

impact they can have on a health care provider, secondary sources such as

newspaper articles and personal experiences by those who wish to retain

their anonymity have been digested and adapted into a variety of formats to

encourage the learning process.

Reality Checks present ethical dilemmas that can occur in the health

care setting. These examples illustrate the dilemmas and problems health

care providers may face. The reader should note that any one Reality

Check involving a particular profession generally can be applied to other

health care professions. There are questions at the end of each example and

readers should be able to use the knowledge they have gained from the

information in the book and their practical experiences to answer these

questions.

People Stories were written by patients, family members, and

caregivers and describe real-life experiences. The People Stories are but a

small sample of the wide range of ethical and legal issues in health care.

Cases provide the reader with an understanding of a vast number of

legal and ethical issues, some of which he or she will face in his or her

career. It is anticipated that the reader will learn from these experiences and

 

 

apply their lessons when faced with health care dilemmas. When reviewing

the various cases in this book, consider both the ethical and the legal

implications of a dilemma and how they intertwine with one another.

Presented here is a sampling of the numerous questions that can be asked

when analyzing an ethical dilemma.

1. What are the relevant ethical and legal issues in the case?

2. What could have been done to bring more clarity to the ethical

dilemma?

3. How should the legal issues of the case be addressed?

4. How might one’s professional code of ethics be violated in the case? 5. Describe how the principles of patient autonomy, beneficence,

nonmaleficence, and justice may have been violated in the case.

6. Discuss the issues that may impact the people involved (e.g., family

members, physicians, other caregivers including nurses, chaplains,

and/or ethics committee members).

7. If you were friendly with the patient, would it affect your ability to give

an objective opinion?

8. Explain how moral values, religious beliefs, education, and life

experiences of both caregivers and patients complicate the resolution of

health care dilemmas.

9. Describe how financial concerns can affect the decision-making

process.

10. Describe how corporate culture can affect the decision-making process.

It should be noted that the book is designed to introduce the student to

various ethical–legal issues and should not be considered an in-depth or comprehensive review of a particular ethical–legal issue.

We study ethics because we need to know right from wrong and

maintain order in a society that would otherwise be lawless. Ethics

distinguishes good from evil. Ethics and the law are inseparable, for it is

ethics that describes our values and morality. An unethical person helps

create a world of fear, distrust, and tyranny. It is the law that describes our

commonly accepted behavior and provides punishment for those who fail

to adhere to the laws of the land. The law describes what is accepted

behavior.

 

 

Each life is like a novel. Filled with moments of happiness, sadness, crisis,

defeat, and triumph. When the last page has been written, will you be

happy or saddened by what you read?

AUTHOR UNKNOWN

*Author’s Note: this text is educational in nature and should not be considered a substitute for legal advice on any particular issue. Moreover, each chapter presents an overview, rather than an

exhaustive treatment, of the various topics. The author, legal reviewers, and/or publisher cannot be

responsible for any errors or omissions, including additions to, interpretation of, and/or changes in

the materials presented in this book.

 

 

NOTES

1. http://www.informaworld.com/smpp/content~content5a794428472~db5all.

 

 

Acknowledgments

I am grateful to the very special people in the more than 1,000 hospitals

and ambulatory sites in 40 states with whom I have consulted, surveyed,

and provided education to over the past 15 years. Their shared experiences

have served to remind me of the importance of making this book more

valuable in the classroom and as a reference for practicing health care

professionals.

This is for my students in ethics and health care law classes at the New

School for Social Research, Molloy College, Saint Francis College, and St.

Joseph’s College as well as my residents while I was an onsite faculty member for George Washington University and those I have instructed

through the years at various seminars, including at the C.W. Post Campus

of Long Island University. I will always be indebted to you for your

inspiration.

The author especially acknowledges the staff at Jones & Bartlett

Learning whose guidance and assistance was so important in making this

publication a reality.

 

 

chapter one

Introduction to Ethics

I expect to pass through this world but once. Any good therefore that I

can do, or any kindness I can show to any creature, let me do it now. Let

me not defer it, for I shall not pass this way again.

STEPHEN GRELLET

LEARNING OBJECTIVES

The reader upon completion of this chapter will be able to:

• Explain what ethics is, its importance, and its application to ethical dilemmas.

• Describe the concepts of morality, codes of conduct, and moral judgments.

• Understand relevant “ethical theories and principles.” • Describe virtue ethics and values and how they more clearly describe

one’s moral character. • Explain why courage is often considered to be the “ladder on which

all other virtues mount.” • Describe why there is a declining trust in the politics of health care. • Understand how religious ethics can affect one’s moral character. • Explain the concept of “situational ethics” and how changes in

circumstances can alter one’s behavior. • Describe the concepts of “ethical relativism” and one’s “moral

compass.”

 

 

INTRODUCTION

Good can triumph over evil.

AUTHOR UNKNOWN

This chapter provides the reader with an overview of ethics, moral

principles, virtues, and values. Ethics and morals are derivatives from the

Greek and Latin terms (roots) for custom. The intent here is not to burden

the reader with the philosophical arguments surrounding ethical theories,

morals, principles, virtues, and values; however, as with the study of any

new subject, “words are the tools of thought.” Therefore, some new vocabulary is necessary for the reader to learn in order to establish a

foundation and apply the abstract theories and principles of ethics in order

to make practical use of them.

 

 

ETHICS

How we perceive right and wrong is influenced by what we feed on.

AUTHOR UNKNOWN

Ethics is the branch of philosophy that seeks to understand the nature,

purposes, justification, and founding principles of moral rules and the

systems they comprise. Ethics deals with values relating to human conduct.

It focuses on the rightness and wrongness of actions, as well as the

goodness and badness of motives and ends. Ethics encompasses the

decision-making process of determining ultimate actions—what should I do, and is it the right thing to do. It involves how individuals decide to live

within accepted boundaries, principles, and values and how we live in

harmony with the environment and one another.

Ethics, also referred to as moral philosophy, is the discipline concerned

with what is morally good and bad, right and wrong. The term is also

applied to any theoretical system of moral values or principles. Ethics is

less concerned with factual knowledge than with virtues and values— namely, human conduct, as it ought to be, as opposed to what it actually is.

Microethics involves an individual’s view of what is right and wrong based on personal life experiences. Macroethics involves a more global

view of right and wrong. Although no person lives in a vacuum, solving

ethical dilemmas involves consideration of ethical issues from both a micro

and macro perspective.

The world is a dangerous place. Not because of the people who are evil;

but because of the people who don’t do anything about it. ALBERT EINSTEIN

 

 

The term ethics is used in three distinct but related ways, signifying (1)

philosophical ethics, which involves inquiry about ways of life and rules of

conduct; (2) a general pattern or “way of life,” such as religious ethics (e.g., Judeo-Christian ethics); and (3) a set of rules of conduct or “moral code,” which involves professional ethics and unethical behavior. The scope of health care ethics encompasses numerous issues, including the

right to choose or refuse treatment and the right to limit the suffering one

will endure. Incredible advances in technology and the resulting capability

to extend life beyond what would be considered a reasonable quality of life

have complicated the process of health care decision making. The scope of

health care ethics is not limited to philosophical issues but embraces

economic, medical, political, social, and legal dilemmas.

Bioethics addresses such difficult issues as the nature of life, the nature

of death, what sort of life is worth living, what constitutes murder, how we

should treat people who are especially vulnerable, and the responsibilities

that we have to other human beings. It is about making the right judgments

in difficult situations.

 

 

Why Do We Study Ethics?

We study ethics to aid us in making sound judgments, good decisions, and

right choices. If not right choices, then better ones. To those in the health

care industry, it is about anticipating and recognizing health care dilemmas

and making good judgments and decisions based on universal values that

work in unison with the laws of the land and our Constitution, and where

the law remains silent, we rely on the ability of caregivers to make right

judgments as guided by the wisdom of Solomon to do good. Doing the

right thing by applying the universal morals and values described in this

text (e.g., the 10 Commandments) will help shield and protect all from

harm.

 

 

MORALITY

Aim above morality. Be not simply good; be good for something.

HENRY DAVID THOREAU

NEWSPAPER CLIPPINGS: Elderly Patient Hit by Motorcycle

Dies in Japan After Being Rejected by 14 Hospitals

After getting struck by a motorcycle, an elderly Japanese man with

head injuries waited in an ambulance as paramedics phoned 14

hospitals, each refusing to treat him.

He died 90 minutes later at the facility that finally relented—one of thousands of victims repeatedly turned away in recent years by

understaffed and overcrowded hospitals in Japan.

Maria Yamaguchi, Associated Press, February 5, 2009

NEWSPAPER CLIPPINGS: Vietnam—Terror of War

Fire rained down on civilians. Women and children ran screaming. Ut

snapped pictures. A little girl ran toward him, arms outstretched, eyes

shut in pain, clothes burned off by Napalm. She said, “Too hot, please help me!”

1973 Spot News, Newseum, Washington, DC

 

 

NEWSPAPER CLIPPINGS: Ethiopian Famine (1985 Feature)

People searched everywhere for food. Some 30,000 tons of it, from the

United States, had been held up by an Ethiopian government

determined to starve the countryside into submission. And starve the

people it did—half a million Ethiopians, many of them children so hungry their bodies actually consumed themselves.

I’ll never forget the sounds of kids dying of starvation.

Newseum, Washington, DC

NEWSPAPER CLIPPINGS: Waiting Game for Sudanese Child

(and a Pulitzer-Winning Photographer’s Suicide)

Carter’s winning photo shows a heartbreaking scene of a starving child collapsed on the ground, struggling to get to a food center during a

famine in the Sudan in 1993. In the background, a vulture stalks the

emaciated child.

Carter was part of a group of four fearless photojournalists known

as the “Bang Bang Club” who traveled throughout South Africa capturing the atrocities committed during apartheid.

Haunted by the horrific images from Sudan, Carter committed

suicide in 1994 soon after receiving the award.

A Pulitzer-Winning Photographer’s Suicide, National Public Radio, (NPR), March 2, 2006

 

 

Trek of tears describes many horrible historic events, from broken treaties

with American Indians to an African Journey of horror, where people

would flee together as a village to escape the barbaric slaughter of men,

women, and children as the remainder of the world stood cowardly by

watching the death and starvation of hundreds of thousands of people.

Human atrocities committed by humans. Is it not time to stand up and be

counted to do what is right and leave all excuses behind for our

complacency toward the genocide that continues throughout the world?

GP

There are those who have been brainwashed into believing, in the name of

religion, that if they blow themselves up in public places, killing innocent

people, that they will be rewarded in the afterlife. This is not religion and

it is not culture; it is evil people brainwashing young minds to do evil

things.

GP

Morality describes a class of rules held by society to govern the

conduct of its individual members. It implies the quality of being in accord

with standards of right and good conduct. Morality is a code of conduct. It

is a guide to behavior that all rational persons should put forward for

governing their behavior. Morality requires us to reach a decision as to the

rightness or wrongness of an action. Morals are ideas about what is right

and what is wrong; for example, killing is wrong, whereas helping the poor

is right, and causing pain is wrong, whereas easing pain is right. Morals are

deeply ingrained in culture and religion and are often part of its identity.

Morals should not be confused with cultural habits or customs, such as

wearing a certain style of clothing. What rules are considered right varies

from nation to nation, culture to culture, religion to religion, and one

person to the next. In other words, there is no universal morality that is

recognized by all people in all cultures at all times.

 

 

Code of Conduct

A code of conduct generally prescribes standards of conduct, states

principles expressing responsibilities, and defines the rules expressing

duties of professionals to whom they apply. Most members of a profession

subscribe to certain “values” and moral standards written into a formal document called a code of ethics. Codes of conduct often require

interpretation by caregivers as they apply to the specific circumstances

surrounding each dilemma.

Michael D. Bayles, a famous author and teacher, describes the

differences between standards, principles, and rules:

• Standards (e.g., honesty, respect for others, conscientiousness) are used to guide human conduct by stating desirable traits to be exhibited and

undesirable ones (dishonesty, deceitfulness, self-interest) to be avoided.

• Principles describe responsibilities that do not specify what the required conduct should be. Professionals need to make a judgment about what is

desirable in a particular situation based on accepted principles.

• Rules specify specific conduct; they do not allow for individual professional judgment.

 

 

Moral Judgments

Moral judgments are those judgments concerned with what an individual or

group believes to be the right or proper behavior in a given situation.

Making a moral judgment is being able to choose an option from among

choices. It involves assessing another person’s moral character based on how he or she conforms to the moral convictions established by the

individual and/or group. A lack of conformity can result in moral

disapproval and possibly ridicule of one’s character.

 

 

Morality Legislated

When it is important that disagreements be settled, morality is often

legislated. Law is distinguished from morality by having explicit rules and

penalties, as well as officials who interpret the laws and apply penalties

when laws are broken. There is often considerable overlap in the conduct

governed by morality and that governed by law. Laws are created to set

boundaries for societal behavior. They are enforced to ensure that the

expected behavior happens.

 

 

Moral Dilemmas

Moral dilemmas arise when values, rights, duties, and loyalties conflict,

and, consequently, not everyone is satisfied with a particular decision. An

understanding of the concepts presented here will help the caregiver in

conflict resolution when addressing ethical dilemmas. Caregivers often find

that there seems to be no right or wrong answer. The best answer when

attempting to resolve an ethical dilemma is based on the wishes known and

the information available at the time a decision must be made. The answer

is often elusive.

 

 

ETHICAL THEORIES

Ethics, too, are nothing but reverence for life. This is what gives me the

fundamental principle of morality, namely, that good consists in

maintaining, promoting, and enhancing life, and that destroying, injuring,

and limiting life are evil.

ALBERT SCHWEITZER

Be careful how you judge others. . . . As Scottish author J.M. Barrie said,

“Never ascribe to an opponent motives meaner than your own.” We tend to judge others based on their behavior, and ours based on our intent. In

almost all situations, we would do well to recognize the possibility—even probability—of good intent in others . . . sometimes despite their observable behavior.

STEPHEN M. R. COVEY, THE SPEED OF TRUST (FREE PRESS)

Ethics seeks to understand and to determine how human actions can be

judged as right or wrong. Ethical judgments can be made based on our own

experiences or based upon the nature of or principles of reason.

Ethical theories and principles introduce order into the way people

think about life. They are the foundations of ethical analysis and provide

guidance in the decision-making process. Various theories present varying

viewpoints that assist caregivers in making difficult decisions that impact

the lives of others. Ethical theories help caregivers to predict the outcome

of alternative choices, when following their duties to others, in order to

reach an ethically correct decision. The paragraphs following provide a

review of the more commonly discussed ethical theories.

 

 

Normative Ethics

Normative ethics is the attempt to determine what moral standards should

be followed so that human behavior and conduct may be morally right.

Normative ethics is primarily concerned with establishing standards or

norms for conduct and is commonly associated with general theories about

how one ought to live. One of the central questions of modern normative

ethics is whether human actions are to be judged right or wrong solely

according to their consequences.

General normative ethics is the critical study of major moral precepts

of such matters as what things are right, what things are good, and what

things are genuine. General normative ethics is the determination of correct

moral principles for all autonomous rational beings.

Applied ethics is the application of normative theories to practical

moral problems. It attempts to explain and justify specific moral problems

such as abortion, euthanasia, and assisted suicide.

Descriptive ethics, also known as comparative ethics, deals with what

people believe to be right and wrong, whereas normative prescribes how

people ought to act.

Meta-ethics seeks to understand ethical terms and theories and their

application.

 

 

Consequential Ethics

The consequential theory of ethics emphasizes that the morally right action

is whatever action leads to the maximum balance of good over evil. From a

contemporary standpoint, theories that judge actions by their consequences

have been referred to as consequential ethics. Consequential ethical

theories revolve around the premise that the rightness or wrongness of an

action depends on the consequences or effects of an action. The theory of

consequential ethics is based on the view that the value of an action derives

solely from the value of its consequences. The goal of a consequentialist is

to achieve the greatest good for the greatest number. It involves asking

these questions:

• What will be the effects of each course of action? • Will they be positive or negative? • Who will benefit? • What will do the least harm?

 

 

Utilitarian Ethics

Happiness often sneaks in a door you did not think was open.

AUTHOR UNKNOWN

The utilitarian approach to ethics involves the concept that the moral worth

of an action is determined solely by its contribution to overall usefulness. It

describes doing the greatest good for the most people. It is thus a form of

consequential ethics, meaning that the moral worth of an action is

determined by its outcome, and, thus, the ends justify the means.

 

 

Deontological Ethics

Act in such a way that you always treat humanity, whether in your own

person or in the person of any other, never simply as a means, but always

at the same time as an end.

IMMANUEL KANT

Deontological ethics is commonly attributed to the German philosopher

Immanuel Kant (1724–1804). Kant believed that although doing the right thing is good, it might not always lead to or increase the good and right

thing sought after. It focuses on one’s duties to others and others’ rights. It includes telling the truth and keeping your promises. Deontology ethics is

often referred to as duty-based ethics. It involves ethical analysis according

to a moral code or rules, religious or secular. Deon is derived from the

Greek word meaning “duty.” Kant’s theory differs from consequentialism in that consequences are not the determinant of what is right; therefore,

doing the right thing may not always lead to an increase in what is good.

 

 

Nonconsequential Ethics

The nonconsequential ethical theory denies that the consequences of an

action or rule are the only criteria for determining the morality of an action

or rule. In this theory, the rightness or wrongness of an action is based on

properties intrinsic to the action, not on its consequences.

Applying this theory to health care decision making, each situation may

have a different fact pattern, thus resulting in moral decisions being made

on a case-by-case basis. The values held ever so strongly in one situation

may conflict with the same values given a different set of facts. For

example, if your plane crashed high in the Andes mountains and the only

source of food for survival would be the flesh of those who did not survive,

you may, if you wish to survive, have to give up your belief that it is

morally wrong to eat the flesh of another human being. Given a different

set of circumstances, given an abundance of food, you would most likely

find it reprehensible to eat human flesh. Thus, there are no effective hard-

and-fast rules or guidelines to govern ethical behavior.

 

 

Ethical Relativism

The theory of ethical relativism holds that morality is relative to the norms

of the culture in which an individual lives. In other words, right or wrong

depends on the moral norms of the society in which it is practiced. A

particular action by an individual may be morally right in one society or

culture and wrong in another. What is acceptable in one society may not be

considered as such in another. Slavery may be considered an acceptable

practice in one society and unacceptable and unconscionable in another.

The administration of blood may be acceptable as to one’s religious beliefs and not acceptable to another within the same society. The legal rights of

patients vary from state to state, as is well borne out, for example, by

Oregon’s Death with Dignity Act. Caregivers must be aware of cultural, religious, and legal issues that can affect the boundaries of what is

acceptable and what is unacceptable practice, especially when delivering

health care to persons with beliefs different from their own. As the various

cultures of the world merge together in common communities, the

education and training of caregivers become more complex. The caregiver

must not only grasp the clinical skills of his or her profession but also have

a basic understanding of what is right and what is wrong from both a legal

and ethical point of view. Although decision making is not always perfect,

the knowledge gained from this text will assist the caregiver in making

better decisions.

 

 

PRINCIPLES OF ETHICS

You cannot by tying an opinion to a man’s tongue, make him the representative of that opinion; and at the close of any battle for principles,

his name will be found neither among the dead, nor the wounded, but the

missing.

E. P. WHIPPLE (1819–1886)

Ethical principles are universal rules of conduct, derived from ethical

theories that provide a practical basis for identifying what kinds of actions,

intentions, and motives are valued. Ethical principles assist caregivers in

making choices based on moral principles that have been identified as

standards considered worthwhile in addressing health care–related ethical dilemmas. Ethical principles provide a generalized framework within

which particular ethical dilemmas can be analyzed and decisions made.

Caregivers will find that difficult decisions often involve choices between

conflicting ethical principles, as described in the following sections.

 

 

Beneficence

Beneficence describes the principle of doing good, demonstrating kindness,

showing compassion, and helping others. In the health care setting,

caregivers demonstrate beneficence by providing benefits and balancing

benefits against risks. Beneficence requires one to do good. Doing good

requires knowledge of the beliefs, culture, values, and preferences of the

patient—what one person may believe to be good for a patient may in reality be harmful. For example, a caregiver may decide to tell a patient

frankly, “There is nothing else that I can do for you.” But what if the patient really wants encouragement and information about care options

from the caregiver? Compassion here requires the caregiver to tell the

patient, “I am not aware of new treatments for your illness; however, I have some ideas about how I can help treat your symptoms and make you more

comfortable. In addition, I will keep you informed as to any significant

research that may be helpful in treating your disease processes.” Paternalism is a form of beneficence. It occurs when individuals and/or

institutions (e.g., political, military, organizational, religious) believe they

know what is best for others, thus making decisions for others. Paternalism

may involve, for example, prohibiting or requiring certain actions.

Medical paternalism can involve making choices for a patient by

withholding medical information, preventing the patient from making an

informed decision. Justification for such actions can occur because of one’s age, cognitive ability, or level of dependency. Physicians are often in

situations in which they can influence a patient’s health care decision simply by selectively telling the patient what they believe to be in the

 
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BCHS3201: Microarray Paper

BCHS3201: Microarray Paper

Background

You will be working with data generated using Affymetrix Arabidopsis thaliana (ATH1) full genome chips. Please watch the microarray lecture posted in Blackboard for information on how the chips are constructed and how they are used. Step-by-step instructions are provided here for managing the data. While I have provided details here, keep in mind that in a real research lab, you would have to decide for yourself how to organize the data and make sense of it.

Arabidopsis thaliana

Arabidopsis thaliana is a small, flowering plant found all over the world. It is commonly considered a weed in the United States and can be found in the Midwest (Texas is too hot; the plant likes temperatures around 68°F). Arabidopsis serves as a model plant because it has a number of characteristics that make it amenable to study. The plant is small, reaching only 30 cm in height when full grown. It grows well grows well in both soil and nutrient media making it easier to develop carefully controlled studies (Meyerowitz, 1989). It is easily grown indoors in a laboratory. Crop plants require much larger facilities and land to study. The life cycle of Arabidoposis is only 6 weeks from seed to seed-producing. This allows a much faster pace for experiments than most crop plants where only one generation of plants can be grown in a calendar year (unless your university is fortunate enough to have land on two hemispheres so you can get two growing seasons in). Arabidopsis plants produce thousands of seeds per plant and these seeds are tiny making them easy to store in microcentrifuge tubes in the freezer (Meyerowitz, 1989).

Arabidopsis has a haploid genome of 5 chromosomes consisting of approximately 125 megabases (The Arabidopsis Genome Initiative, 2000). This is a very small genome compared to that of crop species. Maize, for example, is around 2,500 megabases in size (Adam, 2000). Most genes in Arabidopsis exist at a single locus in the genome. Crop plant genomes are large in part because their genomes contain large sections that are duplicated. This makes creating complete knock-outs of a particular gene difficult. Arabidopsis is amenable to genetic manipulations either through traditional cross-breeding techniques or more modern genetic modification techniques (mutation through T-DNA inserts, chemical agents, or CRISPR-CAS9). Studies conducted in Arabidopsis are often directly transferable to crop species as many of the genes have homologues in crop plants. Studying them first in Arabidopsis is easier, cheaper, and faster.

Sugar and Phytohormone Signaling Pathways

Sugars have a role in basic plant metabolism as a carbon source and also play a role as signaling molecules, contributing to the regulation of a number of pathways in plants. The expression of genes involved in mobilization of starch and lipid reserves is usually repressed by the presence of high sugar levels in the plant while genes involved in storage of carbohydrates are upregulated (Jang & Sheen, 1997; Yu, 1999). Soluble sugar levels in plants also play a role in a number of developmental processes including time to flowering (Bernier et al., 1993), shoot to root ratios (Wilson, 1988), and senescence (cells stop dividing and normal biological processes begin to deteriorate) (Dai et al., 1999). The DNA chip data you will be analyzing for class is part of a larger study to elucidate the full impact of sugar signaling in Arabidopsis and to identify potential components of signaling pathways for future study.

Phytohormones are involved in a wide array of plant responses. The plant phytohormones ethylene and abscisic acid are also intertwined with the sugar response signaling pathways.

Ethylene plays a role in a plant’s development as well as its response to environmental conditions. Ethylene has a role in shoot and root elongation, sex determination, petal senescence, and fruit ripening. It also is involved in the plant’s response to flooding and pathogens.

Abscisic acid is involved in preventing pre-mature germination of seeds, root elongation, and stomatal closure. Stomata are pores in the leaf epidermis which control the rate of gas exchange. The pore is surrounded by two bean-shaped guard cells that regulate the size of the pore opening. Abscisic acid plays a critical role in the closure of the guard cells. Plants with mutations in the abscisic acid biosynthesis pathway have a “wilty” phenotype because they are unable to close their stomata during the day when loss of water to evaporative processes is high. The mutant, aba2, has been found to allelic to the glucose insensitive 1 (gin1) mutant (meaning the mutation for both aba2 and gin1 lie in the same gene).

Signaling pathways often work together to fine-tune plant development and responses. Seed germination, for example is finely controlled by antagonist interactions between sugar and abscisic acid which inhibit germination and gibberellin and ethylene which promote germination (figure 1).

Figure 1. Seed germination is controlled by a combination of signals from sugar levels, abscisic acid, gibberellin, and ethylene.

The sugar-insensitive 6 (sis6) mutant is slightly resistant to the inhibitory effects of abscisic acid on germination (Pattison, 2004). When seeds are grown in a petri plate with nutrient medium supplemented with abscisic acid, germination is delayed in wild-type plants. The sugar-insensitive 3 (sis3) mutant is slightly resistant to the effect of abscisic acid in comparison to wild-type (Columbia ecotype) seeds. The abscisic acid insensitive 4-1 (abi4-1) mutant displays precocious seed germination in the presence of abscisic acid, germinating despite the presence of exogenous ABA which should significantly delay germination (figure 2).

 

 

Figure 2. The sis6 mutant is insensitive to the inhibitory effects of ABA on germination. Seeds were sown on the indicated media and grown in continuous white fluorescent light. Germination was scored every 12 hours for four days and then every 24 hours thereafter. Error bar represent the mean ± standard deviation (n=3). This experiment was conducted three times with similar results. From Pattison, 2004.

 

How the Data was Collected for this set of Experiments

In order to conduct a chip experiment, RNA must be collected from the samples. In our experiments, Arabidopsis seeds were surface sterilized, cold treated at 4° C in the dark for three days and then plated on Nytex mesh screens placed in petri dishes containing minimal nutrient media. After 20 hour under continuous light at 21° the nytex meshes were transferred to plates containing either minimal media, or minimal media supplemented with 100 mM sorbitol, 100 mM glucose, 10 µM abscisic acid or 50 µM ACC (ethylene pre-cursor). Seeds were grown on the new media for 12.5 hours and then frozen in liquid nitrogen. RNA was extracted using a phenol/chloroform extraction (Verwoerd et al., 1989). RNA samples were sent to the Molecular Genomics Core Facility at the University of Texas Medical Branch in Galveston for processing.

Part 1. Selecting your experimental conditions

To begin your work on the microarray project, you need to select your topic of study. You need to decide what you would like to examine and then select the appropriate control condition. Your options are in Table 1 below.

Options Topic Control Experimental Developmental Stage
1 Osmotic stress WT minimum WT sorbitol Germinating seeds
2 Osmotic stress WT sorbitol sis 6 sorbitol Germinating seeds
3 Glucose signaling WT sorbitol WT glucose Germinating seeds
4 Glucose signaling WT glucose ein2-1 glucose Germinating seeds
5 Abscisic acid signaling WT minimum WT on ABA Germinating seeds
6 Abscisic acid signaling WT glucose sis4-1 (aba2) glucose Germinating seeds
7 Abscisic acid signaling WT glucose sis5 (abi4) glucose Germinating seeds
8 Ethylene signaling WT minimal media WT ACC (ethylene) Germinating seeds

Table 1. Select your topic of study for the microarray project. Choose one option. Each row represents one possible option. Because the control must be appropriately matched to the experimental condition, you may not mix and match between rows.

Part 2. Identifying differences in gene regulation between control and experimental conditions.

1. Download the spreadsheet corresponding to your selected control and experimental conditions to your computer.

2. Take a few minutes to familiarize yourself with the spreadsheet layout.

Column A: AGI#. AGI stands for Arabidopsis Genome Initiative. Every gene in the Arabidopsis

was assigned a unique identifier during the genome sequencing project. The Affymetrix DNA

chip contains over 22,000 genes representing nearly every known gene in the genome of Arabidopsis.

Column B: Affy Probe Index #. The Affymetrix probe index # refers to the probe array that corresponds to each gene. Each probe array contains 11 pairs of probe to the same gene. One probe in each pair is a perfect match to the gene and the other contains a mismatch in the center of the probe. The software uses the data from the perfect match sets and the mismatch sets to subtract out signal that may have arisen from near (but not quite perfect) matches. The names of the probe sets are based on what was known about the gene sequence at the time the chip was created.

Names ending in means

_at all probes match one known transcript

_a all probes match alternate transcripts from the same gene

_s all probes match transcripts from different genes

_x some probes match transcripts from different genes

 

Notice that rows 2 through 65 do not have AGI#’s and the Probe Index #’s all begin with AFFX. These are the quality control probe arrays for the chip. They are included so that researchers know that there were not technical issues with the chip or samples. A mix of probes that will result in positive and absent calls are included.

 

Signal Columns: Each experiment in this data set was conducted between 3 and 6 times. The

columns that contain the word “Signal” in the header represent the value for the signal reads.

 

Detection Columns: The column to the right of each signal column is the Detection Column.

P= present

A=absent

M=marginal

 

Present means the gene was expressed in the sample, resulting in a measurable signal above a

minimal detection threshold. Absent means the gene was not expressed under the experimental conditions. Marginal means the expression was very near the detection threshold. Marginal calls require further investigation and experimentation to confirm.

 

Converted Detection Columns: The column to the right of each Detection Column is the Converted Detection Column. The PMA calls are converted to a numeric value which allows the researcher to average the detection calls and decide whether or not to include a particular gene in the data set.

P=2

A=0

M=1

 

Descriptions: what was known about the gene at the gene identity or function at the time the Chip was created.

 

3. Open a new Excel file and name it as follows: Lastname_firstname_microarray.

 

 

4. Change the name of Sheet 1 to “control” by right clicking on the tab and selecting “rename” from the pop up menu. Copy and paste all the data from your control sheet into the “control tab”.

 

5. Click the “+” sign to add another tab at the bottom of the Excel sheet. Rename the new sheet “experimental”. Copy and paste all the data from your experimental sheet into the “experimental tab”.

 

6. For both experimental and control conditions, delete the rows containing the controls. These will be the rows at the top (that lack an AGI#).

 

7. Scroll to the right. Skip a column after the “Descriptions” column. Label the next column to the right “AVG control PMA” or “AVG experimental PMA”. Calculate the average PMA call for each gene using the converted detection column values for each condition. For example, if converted PMA detection calls are located in cells E2, I2, M2, an Q2, the formula you enter into the cell would be “=(E2+I2+M2+Q2)/4”. Do this for both your control and experimental sheets. Enter the formula and copy/paste it down the column. The row numbers will change automatically.

 

 

8. Click the “+” sign to add another tab to the bottom of the Excel sheet. Rename the new sheet “combined”.

 

9. Copy the following columns into the “combined” data sheet. You will need to paste “values” for any columns containing formulas. It’s under paste options.

a. AGI#

b. Signal columns for the control

c. Leave a blank column

c. Signal columns for the experimental

d. Leave a blank column

d. AVG control PMA column

e. AVG experimental PMA column

 

10. In the combined data sheet, add another column to the right of your AVG control PMA and AVG Experimental PMA columns.. Label this one “final PMA call”. Type in the formula “=MAX(XX2:XY2) where XX is the column labeled “AVG control PMA” and XY is the column labeled “AVG exp PMA” (substitute your actual column letters for XX and XY). This formula will transfer the maximum value for the two columns to the new “final PMA call column”. The point of doing this is to preserve genes in the data set where there was signal in one of the two conditions. For example, you would not want to delete a gene from the data set because it had an absent call in the control but was upregulated 15 fold in the experimental conditions. By looking at the results using the final column, we can eliminate genes where the signal was not detected in BOTH conditions.

 

11. In the combined spreadsheet, highlight your entire data set. Make sure you pick up all the cells with data. Click “Sort & Filter” in the toolbar. Click custom sort. Check the box on the right in pop-up box that says “My data has headers”. Sort by the “final PMA call” column from smallest to largest. Delete all rows that have a value of zero for final PMA call. This will eliminate all genes that were not expressed in either the control or experimental condition from the data set.

 

12. Add a column to the right of the “Final PMA call” column labeled “AVG control signal” in your combined spreadsheet. Average the values for the signal columns in your control data set. Use the formula =AVERAGE(X2:Y2) where X is the first column with the control signal data and Y is the last column of control signal data. Copy and paste the formula from row 2 all the way down the column. The row numbers will automatically change in the formula.

 

 

 

13. Add a column to the right of the “AVG control signal” column labeled “AVG experimental signal” in your combined spreadsheet. Average the values for the signal columns in your experimental data set. Use the formula =AVERAGE(X2:Y2) where X is the first column with the control signal data and Y is the last column of control signal data. Copy and paste the formula from row 2 all the way down the column. The row numbers will automatically change in the formula.

 

14. Add a column to the right labeled of the “AVG experimental signal” column labeled “AVG control/AVG experimental”. You will divide the average control signal value by the average experimental value using the formula “=XX2/XY2” [where XX is your AVG control signal column (row 2) and XY is your AVG experimental signal column (row2)]. Copy the formula down the column.

 

15. Add a column to the right of the “AVG control/AVG experimental” column labeled T-test. You will calculate whether there is a statistically significant difference between the two conditions. The syntax for this formula is T.Test(array1,array2, tails, type). Array 1 will be the cells containing the signal values for the control. Array 2 will be the cells containing the signal values for the experimental samples. These are NOT the averaged signals but the original values on the left-hand side of your spreadsheet. We will use a 2-tailed T-test. The type will be a two-sample equal variance test which Excel designates as “2”. For example, if the control signal columns were B, C, D and the experimental signal columns were E, F, and G, then the formula to set up in row 2 for the T-Test would be “=TTEST(B2:D2, E2:G2,2,2). Copy the formula down the row to calculate the p-values for the T-Test for each gene.

 

16. Click the “+” sign to add another tab to the bottom of the Excel sheet. Rename the new sheet “final”. Copy all the data from the “combined” spreadsheet into your “final” spreadsheet using the copy and paste value option. This will allow you to go back to the combined sheet to relax the stringency of your data selection if you find you end up with no genes at all in your data set when you complete the following steps.

 

17. Highlight your entire spreadsheet. Click “Sort & Filter” in the toolbox. Click custom sort. Click the “my data has headers” box on the right of the pop-up box. Sort by T-test value from largest to smallest. Delete all genes that have a p-value greater than 0.05. The expression of these genes is not significantly different between the control and experimental conditions and can be eliminated from the data set.

 

18. Highlight your entire spreadsheet again. Click “Sort & Filter” in the toolbox. Click custom sort. Click the “my data has headers” box on the right in the pop-up box. Sort by AVG control/AVG experimental from smallest to largest. Delete all genes that have a fold change between 1.99999 and 0.499999. What you are looking for are genes where the change in expression is two-fold above or below the level for the control condition. You want to keep genes in the data set where the AVG control/AVG experimental value is below 0.5 or lower. These are genes that are UPREGULATED in the experimental compared to the control. The larger number is in your denominator so the numbers are less than 1. You also want to keep genes in the data set where the AVG control/AVG experimental value is 2 or higher. In this case, the genes are DOWNREGULATED in the experimental condition compared to the control condition. Since the larger number is in the numerator, the value is greater than 1. If you do not have any genes with at least a two-fold difference in expression, between control and experimental, relax your conditions and select genes with fold changes between 1.5 and 0.66.

 

19. Change the font color for all of the down-regulated genes to red [AVG control/AVG experimental values above 2 (or 1.5 if you relaxed the conditions)].

 

20. Change the font color for all of the up-regulated genes to green [AVG control/AVG experimental values below 0.5 (or 0.66 if you relaxed the conditions)].

 

21. Determine how many genes were up-regulated and how many were down-regulated.

 

Part 3. Gene Ontology (GO) Biological Process

1. Copy the first column with the AGI#’s into a new Excel sheet. Do not copy the column header. Save the file as a comma delimited file (CSV).

2. Go to https://www.arabidopsis.org/ . Click Search and select Gene Ontology annotations from the drop down menu.

 

3. Click Choose file. Select your CSV file. Click Functional Categorization.

 

4. Click Draw next to “Annotation Pie Chart”. This will generate 3 pie charts: GO Cellular Component, GO Biological Process, and GO Molecular Function. You will include the GO Biological Process chart in your paper. Copy and paste that into your Word file for your paper. When you write your paper, you should discuss anything that stands out to you as particularly interesting given your chosen topic. You do not need to discuss every single category of information appearing in these charts. You may include the other two charts in your paper if there is something in particular that you wish to highlight or tie into your discussion section of the paper but you are not required to do so.

 

Part 4.

Selecting a gene of interest for detailed study.

Information is continuously being added to our knowledge base. Many genes have been identified since the data in this particular data set was first collected. If you want to see if more information is available for a particular gene that has a particularly striking fold change, you can check TAIR, the Arabidopisis Information Resource at https://www.arabidopsis.org/.

Click Search:

 

Click Microarray Element from the dropdown box. Enter your locus identifier in the box (example: At5g01810). Make sure Affymetrix ATH1 is selected (this is the type of chip our data set is from) and click “Get Microarray Elements”.

 

To get detailed information on a gene of interest.

In this example, information about the gene can be found under the annotation.

 

 

You will want to select a gene that from your dataset that is strongly up or down-regulated (a fold change of 3 is preferred but you may go as low as 1.5-fold if necessary for the purpose of this assignment). You need to select a gene that has been studied in the past. Skip ones that are listed as unknown function in both our data set and when you look it up in the search above.

Next, click the search box in the top left corner again and this time select “Genes”. Enter your locus ID (example At5g01810) in the “starts with” box under the Search by Name or Phenotype section. Scroll to the bottom of the page and hit “Submit Query”. Select your locus from the list by clicking on the blue locus identifier.

 

. 

If the gene has been previously studied, a wealth of information will be available on the next page. Information to include in your paper:

1. Gene locus

2. Other names for the gene:

3. Biological Processes in which the gene plays a role (GO Biological Process)

4. The cellular component in which the protein product is expressed (GO Cellular Component)

5. Growth and developmental stages when the gene is expressed

6. The plant structures where the protein product of the gene is expressed

Take a look at the BAR eFP (The Bio-Analytic Resource for Plant Biology electronic fluorescent pictograph) data. This is a browser engine that “paints” data from genomic data sets, such as microarrays, ont pictographs that repsent the experimental samples used to generat the data set. The purpose of the tool is to help researchers develop testable hypothesis based on the enormous amount of data generated by genomics projects. If you click the Data source you have options you can select that will provide you with information on experimental work others have conducted to study this gene. The informationwill be in a nicely illustrated summary form. The original reference will be included on the page as well.

Another example for the same gene:

 

This is a great place to look for information on your gene to use in your narrative. You should cite the original papers if you use the information in this section. You may need to go back to the original paper for details or clarity.

 

 

 

 

Under the Protein Data section, you will find the following information to include in your paper:

1. Protein Length

2. Molecular weight

3. Isoelectric point

4. List of InterPro domains: Create a table of the domains and their function (if the function is known). Click on the links. This will take you out to the InterPro site where you will find info on the domain. The information in the description might provide some useful information to include in your manuscript. In the table, you should indicate a very BRIEF description of whatever you think is most relevant about this particular domain (think about what your microarray experiment was to help you decide what might be the most useful information to include in the table) and the biological process, molecular function or cellular component that is applicable to the domain (see under GO terms). If no information is available, record “none” in your table. Example:

 

 

Domain Brief Description Biological Process Molecular Function Cellular Component
NAF/FISL_domain: IPR018451 Serine-threonine protein kinase that itneracts with calcineurin B-like calsium sensor proteins Signal transduction None none

 

Table 1. Domain ontology from http://www.ebi.ac.uk/interpro/entry/InterPro/IPR018451/.

 

 

All the way at the bottom of the TAIR page, you will find a list of publications related to the gene. Use these publications as references for your paper.

 

Part 4. Write your microarray paper.

Your microarray paper should contain the following components:

1. Title: The title should contain the species name of the organism (Arabadosis thaliana), your topic of experimentation, and a statement about what you were looking for or what data you were generating.

2. Introduction: Be sure to state the purpose of the study, why the experiment was conducted, review previous works of others in the field (integrated seamlessly, not one reference after another). How a microarray works is not needed here. Assume your reader is familiar with this now long-standing, common-place technique. Focus on your topic (osmotic signaling, sugar signaling, phytohormone signaling, or the interplay between sugar and phytohormone signaling).

3. Results:

a. Report the # of genes upregulated and downregulated by 2-fold or higher.

b. Include a table of top ten most highly genes up-regulated and the top ten most highly down-

regulated genes in your experimental condition compared to to control (use your combined

spreadsheet). Also include any genes that you want to discuss in your discussion section. You

may highlight genes in the discussion that show a change in regulation in your experiment

but didn’t make the top 10. Example:

 

Example:

 

AGI # Affymetrix Probe # Fold change p-value in Student’s T-Test Description
At1g20340 255886_at -4.11044 3.33E-03 Plastocyanin, putative
At1g79040 264092_at -4.02826 6.66E-04 Photosystem II polypeptide, putative
At1g32900 261191_at +3.324657 1.19E-05 Starch synthase, putative

 

 

c. Gene ontology data

 

d. All data collected from Part B about your selected gene for deeper study.

 

e. All figures should be labeled and be accompanied by figure legends. The figure should be

referenced in the text (see figure 1).

 

f. Text (in addition to the figure legends) should be present to inform the reader what you did

and to summarize the results collected. No interpretation of the data is included here. Save

that for the discussion.

 

4. Discussion:

a. Recap you results. Take a look at the descriptions for the genes that are up or down regulated. Now look at the review of literature you selected for homework. Are there genes on the list that you would expect to see based on the literature? Looking at the descriptions, are there genes that make sense to see? If you are looking at sugar, are there genes that are obviously part of sugar metabolic pathways or involved in photosynthesis? If you are looking at phytohormones, do the receptors to your chosen phytohormone appear on the list? You might want to pull up journal articles on some of the genes appearing on the list to explain why they might be appearing on your list. Include a few suggestions for future experiments that could be conducted to expand our understanding of your topic based on your results.

5. References: You should no fewer than 6 journal articles (literature review or primary literature) cited.

6. Appendix: You will upload your Excel spreadsheet separately to the Google Drive. Be sure to drop it in the folder for your TA.

General Information:

· Your paper should be in Times Roman or Calibri font, size 12. Paper margin should be 1 inch. Please double-space the paper. The paper should not contain figures or images from any published work. In order to include previously published images, not only must you cite the source, you must also seek permission from both the original authors and the publisher. Unless you are prepared to submit the documentation for these permissions, do not include figures or images that you did not generate using the TAIR page or create yourself.

· The grading rubric is in Blackboard.

 

References:

Adam, D. (2000). Now for the hard ones. Nature 408, 792-793.

The Arabidopsis Genome Initiative (2000). Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815.

Bernier, G., Havelange, A., Houssa, c., Petitjean, A., and Lejeune. P. (1993). Physiological signals that induce flowering. Plant Cell. 5, 1147-1155.

Dai, N., Schaffer, A., Petreikov, M., Shahak, Y., Giller, Y., Ratner, K, Levine, A., and Granot, D. (1999). Overexpression of Arabidopsis hexokinase in tomato plants inhibits growth, reduces photo synthesis, and induces rapid senescence. Palnt Cell 11, 1253-1266.

Jang, J.-C., and Sheen, J. (1997). Sugar sensing in higher plants. Trends Plant Sci. 2, 208-214.

Meyerowitz, E.M. (1989). Arabidopsis, a useful weed. Cell 56, 263-269.

Pattison, D. (2004) Characterization of sugar-insensitive mutants and analysis of sugar-regulated gene expression in Arabidopsis thaliana. [Doctoral dissertation, Rice University]. Rice University Graduate Electronic Theses and Dissertations.https://scholarship.rice.edu/handle/1911/18679

Verwoerd, T.C., Dekker, B.M. M., and Hoekema, A. (1989). A small-scale procedure for the rapid isolation of plant RNAs. Nucleic Acids Res. 17, 2362.

Wilson, J. B. (1988). A Review of evidence on the control of shoot: root ration, in relation to models. Annals of Botany. 61 (4) 433-449.

Yu, S.-M. (1999). Cellular and genetic responses of plants to sugar starvation. Plant Physiol. 121, 687-693.

 
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Annotated Bibliography

Assess sources for your research for your final presentation (for credibility, reliability, and relevance) and list references in proper APA format. That means the sources you use for this assignment should be directly related to the species that you chose in Forum 1 of the class

Assignment Instructions:  The Research Project/Presentation for this class is divided into three major Assignments, 1) annotated bibliography, 2) outline and 3) final presentation. The first part is the annotated bibliography. An annotation is a summary and evaluation, and your annotated bibliography will include a summary and evaluation of some of the sources (or references) you will use for your presentation.

To prepare for this assignment, I recommend that you do the following:

  • Read these directions carefully.
  • Review the sample annotated bibliography provided to you below.
  • Read the grading criteria below. The grading criteria is a detailed evaluation that I will use to assess your performance. It will also help you understand what is expected of you as you prepare your assignment.
  • Message me with any questions!

The reason the annotated bibliography is included as part of the research project is that writing an annotated bibliography is important in that it provides excellent preparation for the final presentation. One of the issues regarding any type of research, especially in biology, is the credibility of the sources used, particularly those obtained from various websites. By forcing you to evaluate each of your potential sources carefully, the annotated bibliography helps you determine if in fact the source you chose is credible and helps you determine how relevant it is to your topic and understand the topic better which will help you develop your presentation.

For this project, you will assess three sources to include:

1) a complete citation for each source,

2) a summary of each source, and

3) an evaluation of each source.

Three sources are required for this assignment (i.e., you are to write an annotation for each source).  However, you must use five or more sources in your final presentation. 

Use this TEMPLATE to summarize and evaluate each of your three sources.

  1. Citation:

Written in APA reference list format. For more help with formatting, see APA handout.

  1. Summary:

What is the purpose of the source, review article, original research? What topics are covered? This section is generally 4-6 sentences that summarize the author’s main point. For more help, see this link on paraphrasing sources.

  1. Evaluation:

After summarizing the article (or research paper or book), it is necessary to evaluate it and state where you found it – its source (e.g., journal, website, etc.).  Briefly answer the following questions in 4-6 sentences:

What is the format or type of source (e.g., peer-reviewed journal paper, website, book)? How reliable is the information in the article, and how credible is the source (e.g., website’s sponsoring organization, journal or book publisher) and the author(s)?

SCIN130 – Introduction to Biology with Lab

 

Annotated Bibliography

 

 

Name:
Course Number:
Presentation Topic:

 

 

 

Source #1

 

Citation

(in APA format)

 

 

 

 

Summary

 

 

 

 

 

 

 

 

 

 

Evaluation

 

 

 

 

 

 

 

 

 

 

 

Source #2

 

 

Citation

(in APA format)

 

 

 

 

Summary

 

 

 

 

 

 

 

 
 

Evaluation

 

 

 

 

 

 

 

 

 

 

 

Source #3

 

 

Citation

(in APA format)

 

 

 

 

Summary

 

 

 

 

 

 

 

 
 

Evaluation

 

 

 

 

 

 

 

 

 

 

American Public University System May 2018

 
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The Epipelagic Is Divided Into Two Components: The Oceanic Waters And The

Question

1 of 25

The epipelagic is divided into two components: the oceanic waters and the

photic zone.

neritic zone.

pelagic realm.

upper photic zone.

subtidal zone.

Question

2 of 25

Most of the primary production carried out in the open ocean is performed by

seaweeds.

kelps.

phytoplankton.

seagrasses.

zooxanthellae.

Question

3 of 25

Net phytoplankton consist mostly of

copepods.

diatoms and dinoflagellates.

nanoplankton.

cyanobacteria (blue-green algae).

nanoplankton and diatoms.

Question

4 of 25

Typically the most abundant group in the zooplankton are the.

larvaceans.

krill.

fish larvae.

nanoplankton.

copepods.

Question

5 of 25

Which of these is least likely to be seen in the epipelagic?

Suspension feeders

Deposit feeders

Primary production

First-level carnivores

Second-level carnivores

Question

6 of 25

Which of these groups builds a mucus “house?”

Copepods

Arrow worms

Larvaceans

Planktonic snails such as pteropods

Snail larvae

Question

7 of 25

Which of the following accounts for about 50% of the primary production in epipelagic waters?

Diatoms

Cyanobacteria

Dinoflagellates

Coccolithophorids

Silicoflagellates

Question

8 of 25

The following are an adaptation to the planktonic way of life except

spines.

small size.

decrease in drag.

substitution of heavy ions by light ones.

gas-filled bladders.

Question

9 of 25

The storage of lipids within the body is an adaptation in plankton since lipids

make cells heavier.

increase body density.

contain air pockets so they help in buoyancy.

contain a larger amount of energy.

are less dense than water.

Question

10 of 25

The neuston consists of animals that

swim against currents.

sink to the bottom portion of the water column.

are top carnivores in the pelagic realm.

spend their entire lives in the plankton.

live at the surface, but remain underwater.

Question

11 of 25

Counter shading is a form of

shading with bioluminescence.

warning coloration.

structural coloration.

protective coloration.

cryptic coloration.

Question

12 of 25

The rete mirabile found in some fishes is involved in.

increasing speed.

decreasing buoyancy.

digesting food.

increasing buoyancy.

conserving body heat.

Question

13 of 25

Zooplankton that migrate vertically

hibernate at night and feed during the day.

feed at the surface during the day, and migrate below the photic zone at night.

feed in the photic zone during the day, and migrate to the surface at night.

stay below the photic zone during the day, and feed at the surface at night.

migrate up and down but always stay below the photic zone.

Question

14 of 25

Most animals in the epipelagic are omnivores. This means that they eat

producers and consumers.

part of the neuston.

zooplankton.

detritus.

phytoplankton.

Question

15 of 25

What is the relationship between dissolved organic matter (DOM) and bacteria in the epipelagic?

Bacteria feed on the DOM, making it available to other animals in the food chain that feed on bacteria.

Bacteria supply most of the DOM.

Bacteria feed on DOM and thus it is unavailable to other animals.

Bacteria cannot utilize DOM and thus feed on detritus, depleting it through most of the epipelagic.

Bacteria cannot utilize DOM, making it available to animals.

Question

16 of 25

The most common limiting nutrient in the ocean is

silicon.

oxygen.

nitrogen.

carbonate.

phosphorus.

Question

17 of 25

The fall bloom in temperate waters is caused when

primary production decreases as nutrients increase.

primary production decreases due to light limitation.

primary production decreases as nutrients decrease.

primary production increases as nutrients increase.

primary production increases as the number of zooplankton increases.

Question

18 of 25

Equatorial upwelling occurs as a result of

temperature changes at the Equator.

the divergence of equatorial surface currents.

the convergence of equatorial surface currents.

winds causing the Ekman transport of surface water offshore.

El Niño conditions north and south of the Equator.

Question

19 of 25

The Southern Oscillation can be best described as

relative changes between two pressure systems.

variation in wind speed over the Pacific Ocean.

relationship between sea-surface and high-altitude pressures.

tidal differences between the Indian and Pacific Oceans.

wind-speed differences along the Equator.

Question

20 of 25

The long spines and projections seen in many epipelagic plankton are used for

feeding.

reproduction.

increasing drag.

increasing buoyancy.

gathering nutrients.

Question

21 of 25

Most epipelagic fish have a tail that is

short and wide.

short and narrow.

short and thin.

high and wide.

high and narrow.

Question

22 of 25

Which of the following adaptations is least likely to be seen in epipelagic fish?

Stiff fins

A smooth, scaleless body

Increased white muscle

Grove in body for fins

Eyes flush with body

Question

23 of 25

The largest source of dissolved organic material (DOM) in the epipelagic is

viruses.

bacteria.

phytoplankton.

zooplankton.

nekton.

Question

24 of 25

The lateral line system in fishes functions in ________________.

sensing vibrations in the water

detecting magnetic lines of force in water

sensing light in aphotic zones

sweeping surrounding water for plankton

bioluminescence

Question

25 of 25

The remote sensing system found in dolphins and some other cetaceans is ___________.

communal mutualistic behavior

extrasensory perception

echolocation

underwater acoustic sensitivity

heightened smell

 

 

 

 
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