Irreducible complexity and the case for INTELLIGENT DESIGN

I was watching TV earlier, flipping channels actually, something I rarely do since I have a DVR, when I stumbled upon a Christian television show about the complexity of life. It was obviously pro-intelligent design, and I was immediately arrested by it due to the high production values and the caliber of the individuals interviewed. Anyhow, I combed the net a bit to bring back some of the main ideas and concepts that were discussed. I'm obviously a bit biased, but I came away from it with a stronger sense of how I.D. can be PROVEN.

According to Dr. Stephen Meyer says that "...neo-Darwanism will not survive the biology of the information age..."

He also asks, "Where did the information in DNA come from?" Yeah, why don't we ask that question when we're teaching the youth of our nation? Oh yeah, because we like to pretend that those questions don't exist AND because people can't seem to talk about such topics without getting upset, angry, sad, elitist, or religiously intolerant. Too bad, because the avoidance of such issues may be the downfall of our nation.

From this point on, most of the info I am pasting in comes from Wikipedia (to keep things as objective as possible). Although I did find ideacenter.org, a pro-ID site. This is not intended to be a thoughtful, full developed post (do I ever do that?!) but simply a spring board or catalyst to get people, including myself, to do more reading and study on biology and how it relates to our understanding of existence and of God.
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Irreducible complexity

(IC) is an argument made by proponents of intelligent design that certain biological systems are too complex to have evolved from simpler, or "less complete" predecessors, through natural selection acting upon a series of advantageous naturally occurring chance mutations. It is one of two main arguments intended to support intelligent design, the other being specified complexity.^[1] It is dismissed by the scientific community^[2] and intelligent design has been referred to as pseudoscience.^[3]

Biochemistry professor Michael Behe, the originator of the argument of irreducible complexity, defines an irreducibly complex system as one "composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning".^[4] These examples are said to demonstrate that modern biological forms could not have evolved naturally. Critics consider that most, or all, of the examples were based on misunderstandings of the workings of the biological systems in question, and consider the low quality of these examples excellent evidence for the argument from ignorance.

Definitions

The term "irreducible complexity" was originally defined by Behe as:

A single system which is composed of several interacting parts that contribute to the basic function, and where the removal of any one of the parts causes the system to effectively cease functioning. (Darwin's Black Box p39 in the 2006 edition)

Supporters of intelligent design use this term to refer to biological systems and organs that they believe could not have come about by any series of small changes. They argue that anything less than the complete form of such a system or organ would not work at all, or would in fact be a detriment to the organism, and would therefore never survive the process of natural selection. Although they accept that some complex systems and organs can be explained by evolution, they claim that organs and biological features which are irreducibly complex cannot be explained by current models, and that an intelligent designer must have created life or guided its evolution. Accordingly, the debate on irreducible complexity concerns two questions: whether irreducible complexity can be found in nature, and what significance it would have if it did exist in nature.

A second definition given by Behe (his "evolutionary definition") is as follows:

An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations). The degree of irreducible complexity is the number of unselected steps in the pathway.

Intelligent design advocate William Dembski gives this definition:

A system performing a given basic function is irreducibly complex if it includes a set of well-matched, mutually interacting, nonarbitrarily individuated parts such that each part in the set is indispensable to maintaining the system's basic, and therefore original, function. The set of these indispensable parts is known as the irreducible core of the system. (No Free Lunch, 285)

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Biological Machines Are God's Inventions (tabernacles of clay):

FAQ: Aren't "biological machines" too different from human-made machines to be considered examples of designed machines?

The Short Answer: No, biological machines provide a good analogy to human designed machines for us to consider both designed. Both do work, and both are often build upon similar designs.

The Long Answer:

From physics, the definition of work is W=F*d (F=force, d=distance). Based on this understanding, the bacterial flagellum as well as cilia perform work: they exert a force and thereby provide mobility. In the literal sense of the word, these are machines: they exert a force over a distance, which is work. Additionally, these machines have many specialized parts that are will integrated with each other, all of which are required to perform the function of mobility (this gets at the idea of IC). This is very much in line with the concept of a machine. Therefore, we suggest that these are true examples of machines in biology and not just mere collections of molecules. These function exactly as man-made machines.

The similarity between cellular machines and human machines is well-reflected in this quote from Bruce Alberts, president of the National Academy of Sciences: "We have always underestimated cells. … The entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines. … Why do we call the large protein assemblies that underlie cell function protein machines? Precisely because, like machines invented by humans to deal efficiently with the macroscopic world, these protein assemblies contain highly coordinated moving parts."
(Bruce Alberts, "The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists," Cell, 92(February 8, 1998): 291) It should also be noted that intelligent design theorists are not the only ones who see 'machine' analogies in the microbiological realm. The bacterial flagellum and the rotary engine provide an excellent comparison of a human-designed machine and a designed machine in biology. As one researcher wrote, "More so than other motors, the flagellum resembles a machine designed by a human" (David J. DeRosier, Cell 93, 17 (1998)). The mainstream literature is rife with references to "molecular machines," (visit the PubMed Search Engine and search for "molecular machines") and rotary motor enthusiasts, unrelated to intelligent design, have found that "Nature Always Does it First" because of the similarities between the bacterial flagellum and the non-Wankel rotary engine.

The intricacy of the bacterial flagellum dispels any notions that they are not like carefully designed machines: "The eukaryotic flagellum is a complex biochemical machine that moves cells or moves materials over the surface of cells, such as in the mammalian esophagus, oviduct or in protozoa. It is composed of over 250 polypeptides that must be assembled into a number of different structures and each structure must be attached with an exact periodicity along the microtubules. Once the flagellum is assembled, each of the components must act in concert and in three dimensions to produce a complex waveform. This review provides an outline of the composition and function of the different structures found in the flagella of Chlamydomonas."
(Susan Dutcher, "Flagellar assembly in two hundred and fifty easy-to-follow steps" Trends in Genetics, Volume 11, Issue 10)

Move Over U.S., Here Comes China...

The Post-American Technology World

By Bruce Sterling June 08, 2008 | 7:25:02 AM

(((I've read enough of these Sputnik-panic engineering reports to be mighty skeptical of them... mostly because they're put together by engineering schools and their answer is always "more engineers.")))

(((But, if you assume this data isn't entirely massaged, it's quite interesting. It's bad news for American tech predominance, as American tech commentators naturally howl aloud, but China's effect on the REST of the tech world is calamitous. The original Communist Sputnik-terror champs, the Russians, don't even *exist* in this competitive world. And as for Japan, the guys who were supposed to clean America's zaibatsu Japan Inc clock 25 years ago, they're in a tailspin that makes America's look like a cakewalk.)))

(((Furthermore, none of China's neighbors seen to thrive much by China's predominance, which to me suggests some kind of instant-noodle anti-China league in the near future. Unless the likes of Malaysia and Indonesia are eager to become economic colonies.))

Link: TPAC - Technology Policy and Assessment Center at the Georgia Institute of Technology.

What's New

HTI 2007 Final Report is Released

A new study of worldwide technological competitiveness suggests China may soon rival the United States as the principal driver of the world’s economy – a position the U.S. has held since the end of World War II. If that happens, it will mark the first time in nearly a century that two nations have competed for leadership as equals.

(((Howls of pain and woe from the Yankee engineeriate:)))

http://www.manufacturingnews.com/news/08/0516/art1.html

The surge of China past the United States as the global technology powerhouse should be a "Sputnik" moment, but it isn't proving to be. For the most part, federal officials and politicians have been silent. As the economy heads into a downturn, both political parties "are jumping all over each other for the instant fix -- the tax rebate," Porter observes. " 'Problem is all solved. Congratulations!' Wow. I think long term there are things that are not amenable to that solution."

The High-Tech Indicator tells a consistent story over the past 15 years of China's authoritarian government setting its mind on achieving global technology and industrial dominance. "China's entire orientation is toward competing," says Porter. "We frown on planning and don't do much, but they have set their mind on it."

China's gains have been dramatic. The country has not stumbled once in 15 years. "There is no real sense that any kind of leveling off is occurring," says Newman. "Most industrialized countries reach a kind of equilibrium, but the study shows no interruptions in China's advance."

China is training more scientists and engineers and is generously funding their research endeavors. The United States is headed in the opposite direction. "The training of scientists and engineers has lagged, and post 9-11 immigration barriers have kept out international scholars who could help fill the gap," says the Georgia Tech indicator study.

The Georgia Tech "technology standing" measure of 33 countries is based upon four factors: national orientation toward technological competitiveness, socioeconomic infrastructure, technological infrastructure and productive capacity. Each of the indicators is based on a combination of statistical data and expert opinions.

China's ascendancy over 33 nations has "changed the world economic landscape in technology," says Porter. Its continued growth and dominance "won't leave much room for other countries."

Adds Newman: "It's like being 40 years old and playing basketball against a competitor who's only 12 years old -- but is already at your height. You are a little better right now and have more experience, but you're not going to squeeze much more performance out. The future clearly doesn't look good for the United States."

(((Unless you look at China's demographics, that is, because with that one-child policy, the Chinese are gonna get old -- like REALLY, REALLY old. Whereas the worst engineering problem the US has is that it shut off the taps of the brain-drain due to scary actions by 19 suicide pilots, then compounded its cornpone paranoia with organized Elmer Gantry anti-science stupidity.)))

(((How many engineers do you know who are rushing off to learn Mandarin?)))

(((Still, maybe China, now so puissant at nanotechnology, will surprise us all with a Chinese Singularity. Imagine all-conquering Vernor Vinge super-AIs that are Communists and speak Chinese. Wowsers.)))

The Power of the Will

The following is a comment I recently left on Spencer's blog post titled "Miracles":

Excuse the funky use of quotation marks you'll see later in this post. I put the big, bold ones at the beginning and end of my comment to Spencer. At the end I posted more of my thoughts along with some links to more reading about the will.

" "We are so easily distracted today..." I think your statement aligns with something I've been studying and pondering a lot lately which is the idea of "mindfulness." One of our greatest challenges is to calm our thoughts and emotions and listen to our truest voice, that part of us that communes with God. Is it the Holy Spirit? Yes. Is it the voice of the Son? Yes. Is it the voice of the Father? Yes. Is it our own voice? Yes. Our "best self," as President Hinckley often put it, is our truest self, that part of us, most often called our "spirit" in the vocabulary of the church, that is all too often suppressed as we are caught away in the business of this world. Obviously we must busy ourselves with temporal matters or our professional lives and households would fall apart, but we must never forget why we are here and what our main objective is. Our goal, as we know, is to return to the Father, and that requires constant mindfulness, constant diligence. Every day, every hour, and, as we progress, every MOMENT we must observe ourselves until our idea of "self" is no longer associated with our body, our thoughts, or our emotions but rather with the WILL of the Savior which is the will of the Father. It's one thing to begin to comprehend this but it is entirely another thing to begin the WORK that this goal requires.

I think members of our church, and many others for that matter, think that if we enter in the way, all we have to do is attend services and do this or that, and then we die and we gain exaltation. The reality, however, is that we enter in the way by developing faith, repenting, and being baptized but the real work comes in enduring. Enduring includes keeping all of the covenants and commandments. We will not keep them perfectly, which is why we require the grace of the Savior, the only being that ever reascended to the Father, thus opening up the possibility of resurrecting, BUT we must do everything we can, through the exercise of our will (thelema) which, of course, everything hinges and why the battle in heaven was fought and is what we continue to fight with now, in order to return to the presence of the Father. It is through the will we open ourselves up to the Son and once we are worth of His presence, we move closer to preparing for the presence of the Father.

For everyone it comes differently and at different times, but once one realizes that the work of salvation and exaltation must be done and must be done NOW, one begins to look at everything differently, including the role of the Savior, the nature and meaning of His sacrifice and atonement, and the time we have NOW, in this life, in this very MOMENT which is continually before us. As you read this, that MOMENT just passed, but NOW you are in the NOW...we are constantly in the NOW. So what are you doing NOW? What am I doing NOW? Until we live in the NOW and exercise our WILL to be one with our Savior's, we will continue to live under the confines of our own ego and the evil spirits of pride, lust, etc. that constantly seek to reside within us.

Wow. I did not mean to write that much. I think I'll pose this on my "other" blog.

Great post, thanks for sparking some thought. It's all about our WILL!"
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More thoughts....
The more I study, pray and meditate, the more fascinated I become with the importance of WILL POWER. Our will is one thing that I believe God never gave us nor will He take away. Our will is the core of who we are as spiritual, eternal beings, or intelligences. God is THE Perfect Will. Although I don't understand yet, somehow His perfect will helped bring us about in terms of our own possibilities of spiritual evolution. In the LDS church we often use the term "agency" to describe the will because it's a little more, I don't want to say accurate, but it's more clear I think in terms of comprehension for the average person because the term "will" is a little more general. Anyway, WILL POWER, the POWER OF THE WILL, AGENCY, etc. this is a vital concept and one we must understand and think about constantly if we expect to progress.

Another thing I touch upon in the comment below which I'd like to briefly flesh out is the idea of "mindfulness." Self-observation is a paramount for the man who desires to enlarge his soul and progress. We are not our thoughts. We are not our emotions. We are not our actions. Now, this is not to say that our thoughts, emotions and actions don't make us who we are. Follow me here. What I mean to say is that beyond everything we think of as ourselves, we are something separate. Is it our spirit? Well, beyond our mind and our body, yes. But is there something beyond even our spiritual body?

The following are teachings from Joseph Smith regarding the nature of man:

Intelligence Exists Eternally

"Is it logical to say that the intelligence of spirits is immortal, and yet that it has a beginning? The intelligence of spirits had no beginning, neither will it have an end. That is good logic. That which has a beginning may have an end. There never was a time when there were not spirits; for they are co-equal [co-eternal] with our Father in heaven. . . .

Intelligence is eternal and exists upon a self-existent principle. It is a spirit from age to age and there is no creation about it. . . ." (HC 6:311.)

What I take from this is that beyond our spiritual bodies, or our spirits, we are intelligence. A spark of light that never started nor will ever end. Now, for those you who are not LDS or are unfamiliar with this concept, this is not something entirely unique to "Mormon doctrines" nor was Joseph Smith the first to teach this. This particular concept is ancient; indeed, this idea is older than ancient. I call it truth, but that's me!

Here's an excerpt from "Teaching of Joseph Smith" by Truman Madsen.

"CREATION AND COSMOS. Joseph Smith's teachings have been characterized by the word "eternalism": "Every principle that proceeds from God is eternal" (TPJS, p. 181). The "pure principles of element" and of intelligence coexist eternally with God: "They may be organized and re-organized, but not destroyed" (TPJS, p. 351). God created the universe out of chaos, "which is Element and in which dwells all the glory" (WJS, p. 351). "The elements are the tabernacle of God" (D&C 93:35). God is related to space and time, and did not create them from nothing. Change occurs through intelligence. The universe is governed by law. There were two creations: All things were made "spiritually" before they were made "naturally" (Moses 3:5). Through his Son, God is the Creator of multiple worlds. God is the Father of the human spirits that inhabit his creations. His creations have no end. (See Creation home page)"

So here's the cool part, but also the part that I am still trying to understand: God did not "create" us in the sense that there was nothing, and then bam! there we were. But, in some sacred way, God is the Father of Our Spirits. Through some miraculous and holy process, He endowed our eternal selves with something that made us His sons and daughters and set us in the way of eternal progression but with the express intent of always allowing us the right to choose for ourselves, which is our WILL...he didn't give us our WILL, nor would (could) He take it, because that's what allows us to become like Him IF we CHOOSE to. That's why Lucifer, the Son of the Mourning, fell and became the devil. He wanted to take away the will of God's other children, He wanted the glory for himself...his PRIDE, his EGO caused him, even one of the elect, one of the most advanced spirit children of our Father, to spiral down to "hell," to that place in which fear and all other negative emotions rule. He used his will to become Satan, the father of all lies.

We, on the other hand, chose to follow the plan of the Savior, the one we call Jesus Christ. The Holy One of Israel. The only begotten of the Father. THE Master. His plan was to give us the choice, to let us retain our agency, which is the only true way, and knowing we would use our will selfishly and allow fear, lust, pride, anger, etc. to enter into our hearts, would provide Himself as a sacrifice, a perfect sacrifice, to fulfill the natural law of justice that pervades the universe and thus ensure for us a way, if we choose, to reenter the presence of the Father BUT this time knowing good from evil (for initially, in His presence, we were like little children and didn't know the good from the evil nor had we ever had the chance to live in the world of dense matter with physical bodies) and thus to become like Him, beings of truth, light and love who tasted of the darkness but chose to cast it out completely and to become perfected.

Not all beings, however, choose this path. That is why we believe in "multiple levels" or heavens or dimensions or planes of existence. There are different glories for different beings. To become an exalted being, to become like our Father who, by the way, will always be our Father and our God (we don't believe in anyway that becoming like God makes us better than Him, etc.)...to become like Him requires that one cast away all imperfections and completely destroys the ego. The life and teachings of the Savior make it abundantly clear that He, Jesus, had aligned His will so completely with the Father that there was/is NO DIFFERENCE. They are ONE. And, if you recall, the Savior tells us that we must become perfect, even like unto Him and that we can become one with He and the Father.

I will add the scriptural references to this later, but I'm about to fall asleep, so I'll amend this later. If you made it this far, thanks! I hope that something I share here will be of assistance to you as you strive on the path. I have great compassion for all of my fellow beings and feel a strong sense of love and respect for my brethren of all faiths who strive to be true to themselves and to God.

The kingdom of Heaven is within!

Luke 17:

20 ¶ And when he was demanded of the Pharisees, when the ^akingdom of God should come, he answered them and said, The kingdom of God cometh not with observation:

21 Neither shall they say, Lo here! or, lo there! for, behold, the ^akingdom of God ^bis ^cwithin you.

John 17: 11, 21

11 And now I am no more in the world, but these are in the ^aworld, and I come to thee. Holy Father, keep through thine own name those whom thou hast given me, that they may be ^bone, as we are.

3 Ne. 11: 27, 29, 36

27 And after this manner shall ye ^abaptize in my name; for behold, verily I say unto you, that the Father, and the Son, and the Holy Ghost are ^bone; and I am in the Father, and the Father in me, and the Father and I are one.

It's been a while...

Between school, work, laziness, I haven't been here much lately, but I vow to put some time in here once I get my questionnaires out for the research I'm working on right now. Lately I have been thinking about (and trying to put into action) the following principles:

-will power/self-discipline
-self-observation/awareness
-charity/not judging others

The work associated with these principles is EXTREMELY difficult, as I think anyone who is striving to walk on the straight path knows. In one moment you may be very self-aware and in the next moment a particular thought or emotion knocks you completely out of focus and you find yourself unaware of your thoughts or actions which, of course, can lead to a poor choice which can range from a wayward thought or an unkind word. Practice, however, makes perfect and prayer and meditation are the best ways to remain focused and self-observant.

Time for bed! I don't know why I always do this on Sunday nights (it's the long naps I am often able to take after church).