Jamie Hale

Jamie Hale

Saturday, July 18, 2009

The Story of Science

The Story of Science
By Jamie Hale

One night while watching TV I stumbled across a program that featured Joy Hakim.
Hakim is an award winning writer who has written a series of book on US History and Science. After a couple of months of email exchanges I decided it was time to do an interview with Joy Hakim.

What does a day in the life of Joy Hakim look like?

When I'm writing (which is most of the time) I read the NYTimes with breakfast and then get to my desk (usually about 8:30 a.m.). I work until noon, trying to remember to get up every hour and stretch. Then lunch and--this is where my schedule varies--sometimes I do errands, or swim, or go to a yoga class, or go back to work. Sometimes I write into the evening, sometimes I play.

Of the books you have written do you have a favorite?

The book I'm currently working on is always my favorite. But I'm perhaps most proud of "Einstein Adds A New Dimension." It stretched my head and gave me a chance to get to know a wonderful MIT author/physicist, Edwin Taylor.

Was it harder to write the US History books or the science books?

The science books were harder to write because I had little background in the subject. I was trained as a journalist, so no subject intimidates me, still, quantum theory and relativity were tough. I'd like teachers to feel they can tackle any subject by being willing to learn along with their students. The old model of teacher as ultimate expert is out-of-date. Knowledge is increasing at exponential rates, no one can keep up. Teaching students how to find information and process it needs to become the ultimate school goal. If we can create real learning communities in our classrooms we can handle the abundance of information that is now available to all of us everywhere.

Did you have a team of researchers working with you on the history and science series?

I don't have any researchers helping me, I do contact lots of experts and have them read copy and answer questions. It's wonderful, when you are writing for young readers the best people are willing to help

What can we do to improve America’s History and Science programs in our schools?

We need to stop thinking of history and science as isolated stand-alone subjects. History is a great mother discipline. Everything that happens today will be history tomorrow. So history can tie all subjects together. It should be central to curricula. As to science, we live in the greatest scientific era ever. The scientific discoveries of recent times underlie and guide our society. And yet we keep today's most exciting science as an elite subject for a small percentage of our population. No wonder school seems irrelevant to many kids. Black holes, dark matter, dark energy are all out there ready to entice young minds. For heavens sake, why aren't we teaching physics and genetics to all our children? Teachers aren't trained in those subjects? Then they can learn with their students and tie the subject to history and literature too

Why is there such a huge lack of critical thinking courses offered in most school systems?

I don't think much of critical thinking courses. You learn to think critically by researching and writing. I have some experience in those disciplines. I promise--demand more research-based writing and critical thinking scores will soar.

What is your favorite book? Who is your favorite author?

I'm an eclectic reader and love to mix the ancients with 19th century fiction, but mostly I read current books for information, so it is in nonfiction that I spend much of my reading time. We have a group of science writers today who are astonishingly eloquent--they include Hans Christian von Baeyer, Alan Lightman, Richard Feynman, Marcia Bartusiak, and Brian Greene--for starters. Stephen Hawking and his daughter have written adventure books for young readers on space exploration, and they are page-turners. Among historians, David McCullough and Joseph Ellis are favorites. Christopher Buckley's recent book about his parents is a writer's gem. I just finished Jenny Uglow's wonderful book The Lunar Society, about a group of outrageous and amazing 18th century thinkers and doers.

Are you currently working on any new projects?

Yes, right now I am working on two books that are complementary approaches to biology and its process of change. I'm learning a lot.

Visit Joy Hakim's site at www.joyhakim.com

Sunday, July 5, 2009

Quotes that Matter

A few of my favorite quotes

Carl Sagan

But the fact that some geniuses were laughed at does not imply that all who are laughed at are geniuses. They laughed at Columbus, they laughed at Fulton, they laughed at the Wright Brothers. But they also laughed at Bozo the Clown.

For me, it is far better to grasp the Universe as it really is than to persist in delusion, however satisfying and reassuring.

I am often amazed at how much more capability and enthusiasm for science there is among elementary school youngsters than among college students.

Science is a way of thinking much more than it is a body of knowledge.

From Sagan’s Baloney Detection Kit
Arguments from authority carry little weight (in science there are no "authorities")

Wherever possible there must be independent confirmation of the facts

Encourage substantive debate on the evidence by knowledgeable proponents of all points of view

Try not to get overly attached to a hypothesis just because it's yours

Ask whether the hypothesis can, at least in principle, be falsified (shown to be false by some unambiguous test). In other words, it is testable? Can others duplicate the experiment and get the same result?

Aristotle

A friend to all is a friend to none.

Pleasure in the job puts perfection in the work.

Karl Popper

In so far as a scientific statement speaks about reality, it must be falsifiable; and in so far as it is not falsifiable, it does not speak about reality

Socrates

If a man is proud of his wealth, he should not be praised until it is known how he employs it.

Plato

Honesty is for the most part less profitable than dishonesty

Rhetoric is the art of ruling the minds of men

The learning and knowledge that we have, is, at the most, but little compared with that of which we are ignorant

We can easily forgive a child who is afraid of the dark; the real tragedy of life is when men are afraid of the light

Thomas Edison

Genius is one percent inspiration and ninety-nine percent perspiration

Show me a thoroughly satisfied man and I will show you a failure

There is no substitute for hard work

To have a great idea, have a lot of them

We don't know a millionth of one percent about anything

Your worth consists in what you are and not in what you have

Noam Chomsky

Either you repeat the same conventional doctrines everybody is saying, or else you say something true, and it will sound like it's from Neptune

The United States is unusual among the industrial democracies in the rigidity of the system of ideological control - "indoctrination," we might say - exercised through the mass media.

Galileo

All truths are easy to understand once they are discovered; the point is to discover them.

Ben Franklin

Being ignorant is not so much a shame, as being unwilling to learn

He that is good for making excuses is seldom good for anything else

It is the eye of other people that ruin us. If I were blind I would want, neither fine clothes, fine houses or fine furniture

Never leave that till tomorrow which you can do today

Tell me and I forget. Teach me and I remember. Involve me and I learn.

Albert Einstein

Everyone should be respected as an individual, but no one idolized

A man should look for what is, and not for what he thinks should be

Few are those who see with their own eyes and feel with their own hearts

I have no special talent. I am only passionately curious

Insanity: doing the same thing over and over again and expecting different results
It is a miracle that curiosity survives formal education

Whoever is careless with the truth in small matters cannot be trusted with important matters

George Washington

It is better to offer no excuse than a bad one

Rene Descartes

It is not enough to have a good mind; the main thing is to use it well.

Jean Pigaet

Scientific knowledge is in perpetual evolution; it finds itself changed from one day to the next. Scientific thought, then, is not momentary; it is not a static instance; it is a process

George Carlin

Religion has actually convinced people that there’s an invisible man – living in the sky – who watches everything you do, every minute of every day. And the invisible man has a special list of ten things he does not want you to do. And if yu do any of these ten things, he has a special place, full of fire and smoke and burning and torture and anguish, where he will send you to live and suffer and burn and choke and scream and cry forever and ever ‘til the end of time. . . But He loves you

Thursday, June 25, 2009

Moral Life In a Random World

by Dr. Jeff Schweitzer

The very foundation of our moral code is fundamentally flawed. The current code of ethics predominant in modern societies, shaped largely by divine command theory, is based on false promises of eternal salvation or threats of damnation, not on a morality inherent to the human condition. As a result, a moral vacuum has developed, creating a society with deeply-rooted destructive behavioral maladaptations. War, overpopulation, unrelenting poverty, destruction of the environment, indifference to the needs and rights of other life forms and intolerance of our fellow humans all result, to an important extent, from an obsolete religious moral code.

Human beings are not inevitable, and our brief existence is not preordained to be extended into the distant future. If Homo sapiens is to have a continued presence on earth, humankind will reevaluate its sense of place in the world and modify its strong species-centric stewardship of the planet. Our collective concepts of morality and ethics have a direct impact on our species’ ultimate fate.

That religious morality has failed is made clear by humanity’s current fate, and the sad state of the planet. Religion has had 2000 years to prove itself worthy as a guiding moral force. Yet the result of that 2000-year experiment is war, poverty, hunger and suffering across the globe as humanity consumes itself; in addition, after two millennia, we see over-population, depletion of non-renewable resources, and accelerated degradation of the environment because our current moral foundation is not suited to guide us away from that destruction.

Our inner life, our own thoughts, our acts of kindness, and our responsibility and honesty are immune to the random events in the world around us, blind to the inherent purposelessness of the universe. The world can be seen with amazing clarity upon realizing that life is not manipulated by some unseen force, but instead is guided by an individual's power to make decisions and a personal choice to be moral. There is tremendous joy in understanding that the purpose and meaning of life are self-derived.

Many of humanity’s problems originate in the hubris of imagining ourselves at the center of the universe, separate from and better than other animals. But human beings are neither special nor inevitable. As a minor branch on a vast evolutionary bush, modern humans have been roaming the earth for no more than a few hundred thousand years of the earth’s 4.5 billion year history. If the earth’s lifespan were one year, humans would come on the scene only during the last 50 minutes of the year. Ours has been a truly brief presence, barely a cameo on the stage of life, with too little time to demonstrate if the evolution of large brains is a successful strategy for long-term survival of the species.

When Charles Darwin published On the Origin of Species in 1859, he exposed the world to a momentous discovery every bit as significant and disorienting as when Copernicus discovered that the earth was not the center of the universe. For the first time in history, human beings were seen not as creatures of divine origin, but instead as a natural product of evolution, an animal like every other on the planet. Imagine yourself back in that amazing year. The day before Darwin’s book was published, you woke up thinking yourself the image of God; the next morning you realize you have the face of a monkey. Not everybody immediately embraced this rude demotion. Resistance to the idea was inevitable. But have absolutely no doubt: evolution is one of the most extraordinary, successful, thoroughly documented scientific discoveries in human history. Evolution through natural selection is an indisputable fact, just as we now know that the earth revolves around the sun.

Thanks to Darwin, natural selection allows us to understand the development of nature's diversity and complexity without resorting to divine intervention. Through Darwin’s insights, we can understand that life on earth began as a natural event, and that evolution is a random process with no direction or drive. The male peacock would probably agree that any rational design would have relieved him of the burden of a ridiculously large tail, which leaves him vulnerable to predation. But because natural selection is uncaring, the poor bird now has a tail just big enough to attract painfully picky females (something to think about the next time you are pumping iron at the gym), and just small enough to make the competing male next door a greater temptation as somebody’s lunch.

Perhaps unwittingly referring to bacteria, Mathew 5:5 says that “Blessed are the meek, for they will inherit the earth,” and indeed they shall. For regardless of the fate of humanity, bacteria will survive. Bacteria can easily live without us, but we would die quickly without them. If we were able to kill every bacterium in our body, we would be dead within a month. It is the height of folly to claim that evolution was driven toward humans anymore than toward any other living being. Humans are nothing but a short-lived biological aberration, with no claim to superiority. If evolution had a pinnacle, bacteria would rest on top. When the human species is a distant memory, bacteria will be dividing merrily away, oblivious to the odd bipedal mammal that once roamed the earth for such a brief moment in time. Our claims to superiority and our self-promotion to the image of god are simply embarrassing in the face of the biological reality on the ground. There is a loss of credibility when you choose yourself for an award.

The human brain is extraordinarily adept at posing questions, but simply abhors the concept of leaving any unanswered. We are unable to accept “I don’t know” because we cannot turn off our instinct to see patterns and to discern effect from cause. We demand that there be a pattern, that there be cause and effect, even when none exit. So we make up answers when we don’t know. We develop elaborate creation myths, sun gods, rain gods, war gods, and gods of the ocean. We believe we can communicate with our gods and influence their behavior, because by doing so, we gain some control, impose some order, on the chaotic mysteries of the world. By making up answers to dull the sting of ignorance, we fool ourselves into thinking we explain the world. Religion was our first attempt at physics and astronomy.

The idea of powerful gods controlling each important aspect of our lives would not by itself be satisfying. We want to put a face to the power; we want to be familiar with the deities that control our fate; we want to know them so that we can communicate with them and solicit their interventions. We are all Dorothy in the Wizard of Oz, seeking to reveal the nature of god, hoping to strike up a conversation with whoever is in charge. By no coincidence then do our gods take on human form, usually idealized. Male gods are typically buff, in great shape, with washboard abs and thick biceps, while their female counterparts conform to the ideas of beauty at the time, usually in all cases sporting large breasts.

Advances in science, which explain the mysteries of nature’s wrath, remove the need for multiple gods of rain, sun and harvest. If we know the sun is a star sustained by thermonuclear reactions, we need not invoke a sun god. If we know that rain is caused by evaporation and condensation, we can discard our rain god. We understand that thunder is caused by lightning as a consequence of atmospheric ionization, relegating Thor to the pantheon of gods now myth. As gods are the child of ignorance, knowledge is a lethal potion strong enough to kill the most powerful force.

We will show that morals are not derived from religion, nor god’s grant of free will, but instead arise from inherent characteristics embedded in human nature as a consequence of our sociality. What we view as moral behaviors – kindness, reciprocity, honesty, respect for others – are social norms that evolved in the context of a highly social animal living in large groups. The evolution of these social norms enabled a feeble creature to overcome physical limitations through effective cooperation. Morality is a biological necessity and a consequence of human development. Religion, however, has masked and corrupted these natural characteristics with a false morality that converts intrinsic human benevolence and generosity into cheap commodities to be purchased with coupons for heaven. Good behavior is not encouraged as a means of advancing our humanity, but instead is enforced with threats of eternal damnation.

About Jeff Schweitzer

He is the Author of the upcoming book Beyond Cosmic Dice – Moral Life In A Random A World. Dr. Schweitzer served at the White House for the Clinton Administration
Working under President Clinton, Dr. Schweitzer was assigned to provide scientific and technological policy advice and analysis for the President of the United States, Vice President Al Gore and the Director of the OSTP, and to coordinate the U.S. government's international science and technology cooperation (working with the president's cabinet and 22 technical agencies) in countries throughout the world. Visit his website @ www.jeffschweitzer.com

Tuesday, June 16, 2009

Introduction to Skeptical Thinking

By Jamie Hale

I recently presented at the Annual JP Fitness Summit in Kansas City. The Summit features some of the top minds in the fitness industry. Topics include any and everything fitness and nutrition related. My presentation addressed a topic that was foreign to the summit. My topic was Fitness Skepticism. How to apply skepticism to the fitness industry? Some of the participants seemed to have a hard time with this line of thought. Skepticism is rarely if ever mentioned in the popular fitness literature. Learning to question and look for evidence could save fitness enthusiasts a great deal of time, money, and embarrassment. When someone like Alan Aragon (nutritionist & author of Girth Control) comes along and destroys your fiction based nutrition protocol you may be a little embarrassed. Especially if you have been working in the industry for a decade.

Before attending the summit I sent my keynotes to a colleague to see if he had any further suggestions on what I should present. He was impressed and told me this information would be excellent to present as an introduction to skepticism to any group not just fitness professionals. Below are my keynotes I used for the presentation.

Seminar Fitness Skepticism: Key Notes

The Fitness Skeptic (Skeptic is derived from the Greek skeptikos, which means "inquiring" or "to look around) applies reason to any and all ideas promoted by the fitness industry or ideas promoted by anyone making fitness claims. Requires evidence before accepting claims. Explain difference between skeptic and cynic.

What is a cynic? Cynics are distrustful of any advice or information that they do not agree with themselves. Cynics do not accept any claim that challenges their belief system. While skeptics are open-minded and try to eliminate personal biases. Cynics Negative views and are not open to evidence that refutes their beliefs. This can lead to dogmatism.

Dogmatism: authoritarian approach to ideas which emphasizes strict adherence to doctrine over rational inquiry. Opposes independent thinking and reason.

The word dogma is derived from a Greek phrase meaning “that which seems to one, opinion or belief”

Skepticism is a key part of science. Science way of thinking, basically way of analyzing information with idea of testing claims. Ideas on science…………
Make use of scientific method

No precise definition for scientific method but in general most agree with the following:
The following is an excerpt from Why People Believe Weird Things (Shermer 1997). “Through the scientific method, we may form the following generalizations:

Hypothesis: A testable statement accounting for a set of observations.

Theory: A well-supported and well-tested hypothesis or set of hypotheses.

Fact: A conclusion confirmed to such an extent that it would be reasonable to offer provisional agreement.”

Important regarding certainty
NO absolute certainty. Humans are fallible.

R.A Lyttleton (Theoretical Astronomy Pro) suggests bead model of truth
This model depicts a bead on a horizontal wire that can move left or right. A 0 appears on the far left end 1 appears on the far right end.

The 0 corresponds with total disbelief and the 1 corresponds with total belief (absolute certainty).

Bead should never reach the far left or right end. The more that the evidence suggests the belief is true the closer the bead should be to 1. The more unlikely the belief is to be true the closer the bead should be to 0.

Important regarding Theory
To a scientist, the word theory represents that of which he or she is most certain; in everyday language the word implies a guess (not sure).

This often causes confusion for those unfamiliar with science. This confusion leads to the common statement “It’s only a theory.”

Regarding scientist vs. non-scientist
Scientist: One whose activities make use of the scientific method to answer questions regarding the measurable universe. A scientist may be involved in original research (Primary Research), or make use of the results of the research of others (termed Secondary Research.

Scientific degree does not necessarily mean scientist

Thinking gone wrong
Why do we accept so much nonsense in absence of evidence? Define faith

Anecdotes are not science
Scientific Jargon does not make a science
Bold Statements and Bold testimonials
Rumors everywhere
Correlation and causation
Emotive words

How to apply logic
Define logic: Concise English Oxford dictionary: science of reasoning, proof, thinking or inference
Structure of logical argument: 1 or more premises (facts) that argument states to lead to conclusion.
Conclusion to be valid all premises must be true
Conclusion could be true even though is it was invalid
Possible to use incorrect logic to reach a conclusion that happens to be true
Need to identify logical fallacies
Structure of argument
Prm 1: if A=B
Prm 2: and B=C
Logical connection: Then we apply (principle of equivalence)
Conclusion: A=C

Common logical fallacies
Ad hominen
Appeal to authority
Argumentum ad antiquitatem / Appeal to tradition (tradition)
Argumentum ad novitatem / Appeal to Novelty (newer is better)
Shifting the burden of proof (claimant insists you disprove)
Argument from personal incredulity (I can’t explain so it can’t be true)
Inconsistency (sometime scientist sometimes not depends on convenience)
Post-hoc ergo propter (A preceded B, therefore A caused B)
Straw man (arguing against position you created, position ez to argue against)
Cherry picking

Ultimate goal for the skeptic is to see evidence and then evaluate the evidence that supports claim. Evidence stands on it’s own merits.

Considerations when look at evidence refer Alan’s book

Ideological immune system
“In day-to-day life, as in science, we all resist fundamental paradigm change” Jay Snelson (social scientist) calls this resistance an ideological immune system. According to Snelson, the more knowledge individuals have accumulated, and the more well-founded their theories have become the greater the confidence in their ideologies.

Consequence we build up and “immunity” against new ideas that do not corroborate previous ones.

Sometimes if we have so much vested interest it is hard to change our stance on a subject

Bser or Liar
Harry G Frankfurt (Moral philosopher) distinguishes in book On Bullshit
Fitness industry questions more Bsers or Liars??

Practical skepticism
Can’t be skeptical all the time
Sometimes better to not be vocally skeptical
Refer to Riniolo’s article The Myth of Consistent skepticism

Practicing skeptical thinking
Take something you have always believed and try to look at it from other side. Gather all available data. Try to counterpoint your own belief. If faith based no need

Inconsistent Rationalist???
Rational people normally but touch touch topic rationality gone. Completely irrational with specific topics such as religion, abortion, death penalty, children etc.

One of the key points I wanted to emphasize was it’s alright to be skeptical. I pointed out the difference between a skeptic and a cynic. I also emphasized that the people that like to villanize skeptics are generally the real villains (quackos, charlatans, Type 1 supplement salesman, etc.) I was cut a little short on time (enough sitting it was time to go outside and jump into the Total Hale Workout) so I didn’t get to finish my presentation. I think the discussion proved beneficial for some while others found it useless. I received some positive feedback while also receiving negative feedback.

Practical implications for the skilled skeptic

Realize that the need to believe, and serve others, are basic human needs

In general our expectations pretty much determine what we see and don’t see (magicians take full advantage of this expectation)

Humans lie and they BS (almost always with a vested interest)

Under specific conditions hallucinations may occur in healthy people

For many people that don’t understand specific phenomena they would rather believe something than say they don’t know

Apply skepticism in a very cautious manner to particular subjects e.g. religion, abortion, death penalty etc.

Realize you can’t be skeptical 100% of the time as there are not enough hours in the day

The skilled skeptic must learn when to keep their questions to themselves if not you will have many enemies (be a Practical Skeptic)

The majority of society does not understand science nor are they interested (they want to know what to think not how to think)

Skilled skeptics understand the rules of logic, the principles of experimentation, experimental design and what constitutes scientific evidence

Human beings are fallible and have a need sometimes have a need to be right

Human beings have a strong need for certainty, security and stability

Human beings have strong social needs (although not all human beings)

Human beings have a strong need for simplicity, easily understandable answers to complex questions

Human beings like to feel important

Skilled skeptics do not make judgments based on insufficient evidence

Skilled skeptics realizes there are varying degrees of certainty but no absolute certainty

Skilled skeptics listen to other people’s ideas with an open mind

Skill skeptics understand all knowledge is tentative

Skilled skeptics are aware of their own personal bias, and aware when their skepticism turns to cynicism

Skilled skeptics habitually question their own beliefs and methods that were used to come to those beliefs

Skilled skeptics are educated on research methodology (this means at an advanced level)

Skilled skeptics avoid Hero Worship (e.g. James Randi says or Michael Shermer says, also referred to as Appeal to Authority Fallacy)

Skilled skeptics realize science does not explain everything nor does it claim to

Skilled skeptics do not fall prey to the Translation Fallacy (this fallacy occurs when the subject being discussed cannot be defined. If you can define the word or topic forget about stating your opinion.)

Sunday, June 7, 2009

Biochemistry 101

The following is an excerpt from Knowledge and Nonsense: the science of nutrition and exercise

Appendix 1: Biochemistry and Genetics

I decided to include this section for all of the biochemistry fans. Many of the terms mentioned in this section are often discussed in scientific texts and research studies. If you read much research, you may occasionally stumble across a word or phrase that you might not understand. I put together this section to help you understand some of those words and phrases. The terms are not presented in any particular order.

Element
These are the fundamental substances that make up the matter of the universe. An element is any substance that can’t be subdivided further by chemical means. Another way of saying this is that an element is composed of only one kind of atom. Examples of elements include oxygen, nitrogen, sulfur, carbon,and calcium.

Atom
This is the smallest part of an element that still retains the chemical and physical properties of that element. Atoms are composed of three types of subatomic particles.
1. Protons: These are positively charged particles found in the center or nucleus of the atom.
2. Neutrons: These are also found in the nucleus but bear no electrical charge (neutral).
3. Electrons: These particles move around the nucleus in orbits. They have a negative electrical charge. Electrons are arranged in shells around the nucleus. Each shell can contain only a finite number of electrons before a new shell must be formed. The first shell is filled when it has two electrons. The second and each
succeeding shell are filled with eight electrons.

Molecule
A molecule is the chemical combination of two or more atoms. Atoms chemically combine by interactions with their respective electron shells. Such interactions are termed bonds, and these bonds are what hold the atoms together. One of the most
important chemical bonds is the covalent bond, which is where two or more atoms share their electrons with one another. This can effectively fill all of the outer shells of the participant atoms,thereby making them extremely stable. A good example is water.

Macromolecules
Macromolecules are large molecules. Many organic molecules are characteristically large and are thus called macro. These macromolecules are usually formed from smaller repeating subunits. Macromolecules are often termed polymers, and the
subunits which compose them are termed monomers. Monomers are assembled into polymers by a special kind of covalent bond forming reaction termed dehydration synthesis or condensation. The name is due to the fact that water is always one of the products.

Hydrogen bonds
These are weak electrical attractions that occur between the hydrogen atoms in a molecule and the oxygen or nitrogen atoms in the same molecules or in separate molecules. Hydrogen bonds are important because they give macromolecules a threedimensional shape, which is critical to their proper functioning.

Basic organic compounds
Organic compounds are those which contain carbon. There are four major classes of organic compounds that are significant to organisms (carbohydrates, lipids, proteins, and nucleic acids).

Enzymes
Enzymes are protein bio-catalysts that speed up reactions but are
not altered by those reactions. Coenzymes are small organic molecules, frequently vitamins. The enormous diversity of proteins ensures that there will be adequate kinds of enzymes for each and every reaction. Each enzyme is specific for one
particular reaction. This means that each of the hundreds of reactions that occur within the cell must have its own enzyme. The types of reactions a cell can execute are dependent upon the kinds of enzymes present. There are six major classes of enzymes.
1. Oxireductases: Catalyze oxidation reduction reactions.
2. Transferases: Catalyze the movement of functional
groups between molecules.
3. Hydrolases: Catalyze the breakdown of polymers by the
addition of water.
4. Lyases: Catalyze the breakdown of molecules but not by
the addition of water.
5. Isomerases: Catalyze internal rearrangements of
molecules.
6. Ligases and synthetases: Catalyze the linkage of
molecules together.

Biological oxidations
Oxidation is a type of chemical reaction in which electrons are removed from an atom or molecule. Reduction is a type of chemical reaction in which an atom or molecule gains electrons. Oxidation and reduction always go together. It is not possible to
have electrons floating freely about. Whenever one molecule is oxidized another must be simultaneously reduced. In other words, the electron removed from one molecule must be transferred to another molecule.

Metabolism
Metabolism by definition is the sum total of all chemical reactions that occur within the cell or organism. It can be generally categorized into two subsections—catabolism and anabolism. Catabolic reactions are breakdown reactions in which
large complex molecules are reduced to smaller fragments (macromolecules are turned into micromolecules). Anabolic reactions are synthesis reactions whereby smaller molecules are joined to form larger or more energetic ones. Catabolic reactions
are exergonic (energy yielding) while anabolic reactions are endergonic (energy consuming). In the cell, catabolic reactions provide the energy necessary to drive the anabolic reactions.

Kreb’s cycle (tricarboxylic acid cycle, citric acid cycle)
Krebs cycle is a series of catabolic reactions occurring in the mitochondrial matrix. The main purpose of these reactions is the transfer of energy carried in the bonds of acetyl-CoA to electron carrier molecules. The molecules receiving the hydrogens and electrons are the coenzymes NAD+ and FAD, which transfer the hydrogens and electrons to the respiratory chain for the phosphorylation of ADP to ATP. Refer to The Biochemistry of Human Nutrition by Sareen Gropper for a detailed description of what happens in the Krebs cycle.

Thermic effect of food
The thermic effect of food (diet-induced thermogenesis) is an increase in the metabolic rate that occurs following the ingestion of food. It is thought to account for an increase in the basal metabolic rate of between 5 percent and 15 percent. The increase in metabolism is a result of increased oxidation associated with the digestion of food, absorption, transport, metabolism, and storage of energy following eating. Protein has the highest thermic effect of the three macronutrients. Carbohydrates have the next highest and fats the least thermic effect.

Nucleic acids
There are two types of nucleic acid—DNA and RNA. DNA is the largest molecule and it has two essential functions. It is the hereditary molecule containing the genetic blueprint that it transmits from generation to generation, and it regulates the
activity of the cell by controlling protein synthesis. All RNA is synthesized off of the DNA molecule. Part of the DNA unwinds and ribose, containing nucleotides, are locked into position in place of the deoxyribose nucleotides. Therefore, all RNA
represents a copy of some of the information contained in the DNA molecule.

Saturday, May 23, 2009

Dangerous Ideas

by Jamie Hale

What is Your Dangerous Idea (Brockman 2007) takes a look at some of the world’s leading thinkers and their most dangerous ideas. Some of the ideas in the book include:

Keith Devlin’s idea we are entirely alone

Devlin suggests there is no higher being and no higher purpose to our lives. Devlin does not see this as a bad thing. He believes the opposite. “The fact that our existence has no purpose outside that existence is completely irrelevant to the way we live our lives, since we are inside our existence. The fact that our existence has no purpose for the universe- whatever that means- in no way means that it has no purpose for us.” I have heard the argument many times if there is nothing else what purpose do we have none. My purpose is to have a happy life and enjoy time with my loved ones. Whether my mark on the universe is significant makes no difference as far as my personal happiness is concerned. I think spending too much time trying to figure out if there is something more de-values the time you have on earth. What is wrong with living your life for you?

Marc D. Hauser’s idea it appears that a wide variety of moral judgments are immune to cultural and demographic variation, including religious background.

Hauser further expands on his idea by saying “Controlling for age, people with only a high school education are no different from people with advanced degrees when it comes to judging the permissibility of harming another person in certain contexts. People with religious backgrounds are no different in this regard from atheists and agnostics.” There are religious people that have high moral standards and there are non-religious people who have high moral standards (depending on how you define moral standards). Classifying people’s morality based on non-religious or religious belief is a logical fallacy (Hasty Generalization). Moral standards are based on the teachings in the bible is common fallacy. Basing moral standards by cherry-picking passages from the bible may give us some moral guidance but the bible as a whole is full of horrible acts.

Bertrand Russell’s idea that it is undesirable to believe in a proposition when there is no ground whatever for supposing it true.

This seems so obvious why should it have to be said. There are many people that believe things with absolutely no valid reason to believe. How many times have you heard just have faith in other words just believe? The essence of faith is believing something in the absence of evidence.

Jordan Pollack’s idea it is a very dangerous idea to consider science as just another religion

Pollack makes it clear this is not his idea but and idea held by some. This is a completely ridiculous statement often perpetuated by religious fanatics. Yet, the differences between religion and science are astounding. I have addressed this numerous times in past articles but to summarize science is evidence based and can actually be tested while religion is faith based and cannot be tested (religion is not science or similar to science in any way shape or form).

Judith Harris’s idea parents have no power at all to shape their child’s personality, intelligence, or the way he or she behaves outside the family home?

Harris says there is no solid evidence that indicates parents shape their children. She doesn’t see this as a bad thing. She says if people accepted these things it would get easier for children and parents. Parents would stop worrying so much about if they are doing the right thing when it comes to raising kids. Kids would appreciate praise more if it weren’t handed out in abundance. I think some kids are influenced by their parents while others seem to be affected very little. I can think of a few instances where parents provided their kids with bundles of attention and love but the kid grew up to be a menace to society. I am also aware of a couple of cases where the parents done a horrible job (in accordance to general standards) parenting but the kids turned out ok.

Matt Ridley’s idea the more we limit growth of government, the better of we will all be.
Ridley says, “In every age and at every time, there have been people who say wee need more regulation, more government. Sometimes they say we need it to protect exchange from corruption, to set the standards and police the rules – in which case they have a point, though often they exaggerate it.” I think in most cases the people that insist more government is needed have a vested interest. Ridely is not suggesting we abolish government but limiting its growth would be a good idea.

Roger Schank’s idea is school is bad for kids

I found Schank’s idea to be the most interesting in the book. I have held this idea for many years. I worked at a junior high school briefly and seen firsthand how disgusted and bored most kids were at school. I think most of them felt the same way I did when I was in school (bored, frustrated, and sleepy). Almost every kid I talk to hates school. Does that make it bad? That’s only part of what makes it bad. Other problems include the curriculum, the methods of testing, over emphasis on rote learning (memorization), unilateral paths of knowledge, under-emphasis on skepticism, grade inflation, compulsory attendance, social pressures, favoritism etc. Schank says, “ Schools should simply cease to exist as we know them. The government needs to get out of the education business and stop thinking that it knows what children should know and then test them constantly to see if they regurgitate whatever they have just been spoon-fed. The government is an always has been the problem in education.” Schank promotes the idea that learning should be guided by passion. Schank’s idea should be a wake up call to you if you are not aware of the state of formal education. Another thing to keep in mind is the common misuse of the word education. Formal Education is often nothing more than a business and it should not be mistakenly considered the only type of education. I would bet that almost anyone that has a wealth of knowledge in their respected field gained most of that knowledge on their own. In fact, even while in school you generally don’t learn in the classroom (if you learn). You simply take directions on what you need to learn out of the classroom (learn studying at home, library etc.). Ralph Waldo Emerson put it like this “We are shut up in schools and college recitation rooms for ten or fifteen years, and come out at last with a belly full of words and do not know a thing.”

Leo Chalupa’s idea what’s needed to attain optimal brain performance- with or without brain exercise- is a twenty-four-hour period of absolute solitude.

This means no writing, reading, phone, watching TV, music or any verbal interactions of any with another human. I tried this but I didn’t make it. I kept thinking about things I needed to write. At around the 16th hour I started writing.

You can check out ideas of some of the World’s leading thinkers at www.edge.org

Tuesday, May 12, 2009

When Good Thinking Goes Bad (Interview)

by Jamie Hale

The following interview was conducted with Todd Riniolo the author of When Good Thinking Goes Bad. Be sure to check out the podcast mentioned at the end of the interview. Good stuff.

Let’s talk about your book When Good Thinking Goes Bad. According to Michael Shermer it’s the perfect primer on critical thinking. What makes it the perfect primer on critical thinking?

I believe it’s a good primer for several reasons. First, the book emphasizes some of the hallmarks of critically evaluating claims in a reader friendly format that should be particularly useful for those who are being exposed to the process of skepticism for the first time. Second, the book also demonstrates how all of us, even when we know how to think critically, will in some instances abandon our skepticism making us more likely to accept foolish beliefs. Lastly, the book was written with students in mind. In fact, I use the book as one of several when teaching a course on skeptical thinking as it relates to paranormal and pseudoscientific claims.

Why is critical thinking so demphasized in our society?

Perhaps because critical thinking takes work. It is much easier in some instances to simply accept information for a variety of reasons. For example, we often do not have the time or motivation to question many claims; especially those that we already believe are true.

Do you feel that formal education programs generally do a good job of teaching critical thinking?

The best teachers are those that teach students the process of critical evaluation, which then allows the student to make up their own mind. Unfortunately, in many instances students are simply told what they should think. Critical thinking is a process, and often times this important element is overlooked.

What is the typical systematic progression in evaluating a claim? Let’s say we want to investigate the global warning crisis. At least some would have us believe crisis.

For any claim, whether it is global warming or psychic claims, the hallmarks of skepticism should be followed. Thus, we must demand evidence and rigorously evaluate the provided evidence. We must seek out expert opinion and employ the proper research methods when appropriate (i.e., double-blind procedures). We must interpret findings with the law of parsimony, and be wary of second hand sources, and so forth. Unfortunately, all of us do not apply the standards of skepticism consistently across claims (we are much more likely to apply the methods of skepticism to claims that we do not believe, while not giving those things we already believe a “free pass”). I point this out in my book by attempting to make a comparison between psychic claims and claims for global warming. This chapter seems to have upset some readers, but the intent was to demonstrate that we are all inconsistent with our skepticism.

Do you think critical thinking comes more naturally to some than others? Or is critical thinking more influenced by nurture?

The old nature versus nurture debate is one in which I can only offer my opinion, so take it for what it is worth. I assume that both nature and nurture play a role. Think about Tiger Woods for a moment. He was born with a predisposition towards a specific skill (i.e., golf). Yet, in order to maximize his potential, he needed to practice, practice, practice. It likely is the same with thinking skills. You have genetic range, which is then influenced by the environmental input.

I heard an interview with you on Point of Inquiry and you pointed out that Santa Claus was a good subject to use when exploring the critical thinking process. Please explain?

Many skeptics over the years have made a variation of the following argument: It’s no wonder that so many people are gullible since we teach our kids about Santa. I find this argument, linking Santa to widespread noncritical thinking in our society problematic on many levels (you’ll have to read the book for more details). Perhaps most disappointing from the skeptics who make this argument is that they provide no evidence (i.e., a peer-reviewed article) and appear to be misinformed about magical thinking in children (yes, there is a literature on this topic!). However, back to the specific question. Many skeptics, such as Carl Sagan, have recommended applied exercises to teach critical thinking. Allowing children to skeptically evaluate the Santa claim on their own, which most eventually do accomplishes that goal. Thus, a long-standing, highly cherished belief (as a kid, who doesn’t want Santa to be real?) starts to become questioned. In fact, most children start to ask critical questions, gather evidence, and develop alternative hypotheses prior to discovering the truth. Isn’t that what critical thinking is all about? I believe that Santa is a useful event for children to practice critical thinking on a widespread, culturally perpetuated myth, in a user-friendly format. For those that disagree, that’s ok. However, there still exists no evidence that Santa is linked with widespread noncritical thinking…

Who will benefit from reading When Good Thinking Goes Bad?

I think two groups. First, the novice, who is looking for an introduction to skeptical thinking. Second, the elite critical thinker. I attempt to demonstrate that even the best critical thinkers are prone to believe in some nonsense. This likely occurs because of the biases that humans possess, which likely provided us with an evolutionary advantage at one point in time, but makes it impossible for any individual to be a consistent skeptic. Thus, labeling ourselves as a skeptic does not guarantee that we will behave like skeptics in all situations, and my book attempts to illustrate this point.

Suppose someone reads this interview and they decide they need to become more skeptical about the world. They want to understand how to apply critical thinking to their everyday life. Where do they start?

There are many excellent resources (Michael Shermer’s work, James Randi’s work, Richard Wiseman’s work, Skeptic Magazine, The Skeptical Inquirer, and so forth). I thought I would provide a resource that is not typically given in an interview like this. I would recommend Thomas Sowell’s Basic Economics, Applied Economics, and Economic Facts and Fallacies. So many of us have such strong opinions about economics issues based upon nothing more than personal experience or what we would like to be true. These books provide a critical look at a topic that is important for all of us, but so few people have taken the time to learn even the basics of the subject.

Some people seem to be very rational most of the time but when it comes to discussing religion their rationality goes out the window. I think sometimes people proclaim beliefs that they really don’t believe. They try to tell themselves they should belief whatever but deep down in they don’t and this creates guilt. Usually because everyone who surrounds them holds this belief (or so they say) they feel social pressures to believe the same. Would you agree? Why are some people rational most of the time but in this particular issue so irrational?

This is a great question, but I would not confine it to religion. If you substitute in “the environment,” “politics,” “dieting,” “multiculturalism,” “male-female differences,” and so forth, the same would apply. In part 2 of my book, I attempt to answer the question of why can a rational person most of the time be irrational on a particular issue. In fact, I would argue that this occurs with all of us, but we are unaware of when we ourselves are the irrational one.

Any other projects you are currently working on?

Glad you asked. I have just finished a rough draft of a book which attempts to answer the question of exactly how did Sigmund Freud first become a household name in America. I believe the parsimonious answer has been overlooked, but do not want to give away the answer. The book is also intended to be a supplemental book when teaching a history of psychology course, as it stresses the important of historical research and that history can be quite exciting!

Can you recommend any sources to help create a more intellectual environment?

“When Good Thinking Goes Bad”!!!!!!!!!

In this discussion with D.J. Grothe, Todd Riniolo discusses his book When Good Thinking Goes Bad www.pointofinquiry.org/todd_c_riniolo_when_good_thinking_goes_bad/