Jamie Hale

Jamie Hale

Tuesday, August 11, 2009

Interview with Carl Zimmer

by Jamie Hale

The following interview was conducted with Carl Zimmer science writer, Yale University Lecturer and author of The Tangled Bank: An Introduction to Evolution. E.O Wilson says " The Tangled Bank is the best written and best illustrated introduction to evolution of the Darwin centennial decade, and also the most conversant with ongoing research. It is excellent for students, the general public, and even other biologists.”

I have completed about 1/2 of your book Soul Made Flesh and I must compliment you on your writing style. Great job. What influenced you to write the book?

CZ: I like to write books about subjects I want to get more familiar with. In this case, I thought I wanted to learn more about the brain. But I didn't want to write yet another book about new developments in neuroscience. It's not that there aren't some great books on that particular subject, but there are so many that I didn't want to get lost in the crowd. It occurred to me that there hasn't been much written about the history of neuroscience. While there is a growing body of scholarship, few authors have written about that research for the public. So I started to nose around and discovered a period of history, in the mid-1600s, that was just incredible in its revolutionary discoveries and also in its political and religious turbulence. This was when the science of neurology was launched, when people came to recognize the brain as we see it today, as the center of our existence. Once I realized this, I knew I had to write the book.

How many books have you written? Do you have a favorite? Which one was the hardest to write?

CZ: I've written seven books now. I suppose my favorite is my first, At the Water's Edge, simply because it gave me the first experience of seeing my name on a book. That's a marvelous feeling.

Commenting on your soon to be released book (The Tangled Bank: An Introduction To Evolution) E.O Wilson says " The Tangled Bank is the best written and best illustrated introduction to evolution of the Darwin centennial decade, and also the most conversant with ongoing research. It is excellent for students, the general public, and even other biologists.” What do you think makes the book so great?

CZ: You'd have to ask Wilson or the other scientists who gave such wonderful endorsements why they like it so much. All I'd say is that it was a huge amount of fun to write, because there are so many fantastic lines of research in evolution these days to choose from. Making the experience even better was the opportunity to work with illustrators and photo editors to make the book as handsome as possible, and to use pictures to explain the science in ways words can't.

Do you think there will come a time in America where the majority of the population will believe in evolution?

CZ: I'm fairly optimistic, in the long term. For now I don't expect tremendous changes, though.

If Darwin were alive today and he were to modify his theory of evolution what would he change?

CZ: I think Darwin would be fascinated by the genome. Genomes are shaped by evolution in all sorts of complex ways. There are even virus-like stretches of DNA that make copies of themselves over time and gradually swamp their host genome. Most of our DNA comes from these genomic parasites. There's also plenty of evidence now that genes have moved many times from one species to another. So genomes are not just sculpted by mutations, drift, and selection from one generation to the next. They're also mosaics, made up of bits of genetic material from many different sources.

What does a typical day in the life of Carl Zimmer look like?

CZ: Breakfast with the family, then trundling off to my home office, where I interview, research, and write till dinner. I punctuate that sedentary work with the occasional trip to visit a scientist in his or her medium--a lab, a bog, a hospital, or wherever they may do their work.

Do you have a favorite writer? Favorite book?

CZ: I do love Melville--both the novels and the stories. The Loom's name is from one of my favorite passages from Moby Dick, where Melville describes how Pip, a cabin boy, was altered by a plunge into the sea:

"...among the joyous, heartless, ever-juvenile eternities, Pip saw the multitudinous, God-omnipresent, coral insects, that out of the firmament of waters, heaved the colossal orbs. He saw God's foot upon the treadle of the loom, and spoke it; and therefore his shipmates called him mad."

About the Author

Carl Zimmer bio http://carlzimmer.com/bio.html

Monday, August 3, 2009

Knowledge Roundup 2

Brain Facts
A Primer on the Brain and Nervous System


Brain Facts is a 74-page primer on the brain and nervous system, published by SfN. Designed for a lay audience as an introduction to neuroscience, Brain Facts is a valuable educational resource
Free Ebook http://www.sfn.org/index.aspx?pagename=brainFacts§ion=publications

Mirror Neurons
You see a stranger stub her toe and you immediately flinch in sympathy. You watch a baseball outfielder run to catch a long fly ball and feel your heart racing and your leg muscles pumping along with him. You notice a friend wrinkle up his face in disgust while tasting some food and suddenly your own stomach recoils at the thought of eating. This ability to instinctively and immediately understand what other people are experiencing has long baffled neuroscientists, psychologists, and philosophers alike. Recent research now suggests a fascinating explanation: brain cells called mirror neurons. Read More http://www.sfn.org/index.aspx?pagename=brainBriefings_MirrorNeurons

The Science of Gossip: Why We Can’t Stop Ourselves

In the past few years I have heard more people than ever before puzzling over the 24/7 coverage of people such as Paris Hilton who are “celebrities” for no apparent reason other than we know who they are. And yet we can’t look away. The press about these individuals’ lives continues because people are obviously tuning in. Although many social critics have bemoaned this explosion of popular culture as if it reflects some kind of collective character flaw, it is in fact nothing more than the inevitable outcome of the collision between 21st-century media and Stone Age minds.

When you cut away its many layers, our fixation on popular culture reflects an intense interest in the doings of other people; this preoccupation with the lives of others is a by-product of the psychology that evolved in prehistoric times to make our ancestors socially successful. Thus, it appears that we are hardwired to be fascinated by gossip. Read more http://www.scientificamerican.com/article.cfm?id=the-science-of-gossip

I want to Believe

In a 1997 episode of The Simpsons entitled “The Springfield Files” — a parody of X-Files in which Homer has an alien encounter in the woods (after imbibing 10 bottles of Red Tick Beer) — Leonard Nimoy voices the intro as he once did for his post-Spock run on the television mystery series In Search of…: “The following tale of alien encounters is true. And by true, I mean false. It’s all lies. But they’re entertaining lies, and in the end isn’t that the real truth? The answer is no.”
Read more http://www.michaelshermer.com/2009/07/i-want-to-believe/

Darwin Myths

Darwin coined the phrase “survival of the fittest” (Herbert Spencer actually coined the phrase)

Darwin was an atheist (no he was agnostic)

Darwin was always an evolutionist which was passed down to him from his grandfather (Darwin was a creationist before and during the voyage of the Beagle and didn’t become an evolutionist until approximately a year after his return. Darwin did not devise his theory while in Galpagos)

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.