DNA: The Tiny Code That's Toppling Evolution

Good News Magazine ^ | May 2005 | Mario Seiglie

[DouglasKC]

DNA: The Tiny Code That's Toppling Evolution

As scientists explore a new universe—the universe inside the cell—they are making startling discoveries of information systems more complex than anything ever devised by humanity's best minds. How did they get there, and what does it mean for the theory of evolution?

by Mario Sieglie

Two great achievements occurred in 1953, more than half a century ago.

The first was the successful ascent of Mt. Everest, the highest mountain in the world. Sir Edmund Hillary and his guide, Tenzing Norgay, reached the summit that year, an accomplishment that's still considered the ultimate feat for mountain climbers. Since then, more than a thousand mountaineers have made it to the top, and each year hundreds more attempt it.

Yet the second great achievement of 1953 has had a greater impact on the world. Each year, many thousands join the ranks of those participating in this accomplishment, hoping to ascend to fame and fortune.

It was in 1953 that James Watson and Francis Crick achieved what appeared impossible—discovering the genetic structure deep inside the nucleus of our cells. We call this genetic material DNA, an abbreviation for deoxyribonucleic acid.

The discovery of the double-helix structure of the DNA molecule opened the floodgates for scientists to examine the code embedded within it. Now, more than half a century after the initial discovery, the DNA code has been deciphered—although many of its elements are still not well understood.

What has been found has profound implications regarding Darwinian evolution, the theory taught in schools all over the world that all living beings have evolved by natural processes through mutation and natural selection.

Amazing revelations about DNA

As scientists began to decode the human DNA molecule, they found something quite unexpected—an exquisite 'language' composed of some 3 billion genetic letters. "One of the most extraordinary discoveries of the twentieth century," says Dr. Stephen Meyer, director of the Center for Science and Culture at the Discovery Institute in Seattle, Wash., "was that DNA actually stores information—the detailed instructions for assembling proteins—in the form of a four-character digital code" (quoted by Lee Strobel, The Case for a Creator, 2004, p. 224).

It is hard to fathom, but the amount of information in human DNA is roughly equivalent to 12 sets of The Encyclopaedia Britannica—an incredible 384 volumes" worth of detailed information that would fill 48 feet of library shelves!

Yet in their actual size—which is only two millionths of a millimeter thick—a teaspoon of DNA, according to molecular biologist Michael Denton, could contain all the information needed to build the proteins for all the species of organisms that have ever lived on the earth, and "there would still be enough room left for all the information in every book ever written" (Evolution: A Theory in Crisis, 1996, p. 334).

Who or what could miniaturize such information and place this enormous number of 'letters' in their proper sequence as a genetic instruction manual? Could evolution have gradually come up with a system like this?

DNA contains a genetic language

Let's first consider some of the characteristics of this genetic 'language.' For it to be rightly called a language, it must contain the following elements: an alphabet or coding system, correct spelling, grammar (a proper arrangement of the words), meaning (semantics) and an intended purpose.

Scientists have found the genetic code has all of these key elements. "The coding regions of DNA," explains Dr. Stephen Meyer, "have exactly the same relevant properties as a computer code or language" (quoted by Strobel, p. 237, emphasis in original).

The only other codes found to be true languages are all of human origin. Although we do find that dogs bark when they perceive danger, bees dance to point other bees to a source and whales emit sounds, to name a few examples of other species" communication, none of these have the composition of a language. They are only considered low-level communication signals.

The only types of communication considered high-level are human languages, artificial languages such as computer and Morse codes and the genetic code. No other communication system has been found to contain the basic characteristics of a language.

Bill Gates, founder of Microsoft, commented that "DNA is like a software program, only much more complex than anything we've ever devised."

Can you imagine something more intricate than the most complex program running on a supercomputer being devised by accident through evolution—no matter how much time, how many mutations and how much natural selection are taken into account?

DNA language not the same as DNA molecule

Recent studies in information theory have come up with some astounding conclusions—namely, that information cannot be considered in the same category as matter and energy. It's true that matter or energy can carry information, but they are not the same as information itself.

For instance, a book such as Homer's Iliad contains information, but is the physical book itself information? No, the materials of the book—the paper, ink and glue contain the contents, but they are only a means of transporting it.

If the information in the book was spoken aloud, written in chalk or electronically reproduced in a computer, the information does not suffer qualitatively from the means of transporting it. "In fact the content of the message," says professor Phillip Johnson, "is independent of the physical makeup of the medium" (Defeating Darwinism by Opening Minds, 1997, p. 71).

The same principle is found in the genetic code. The DNA molecule carries the genetic language, but the language itself is independent of its carrier. The same genetic information can be written in a book, stored in a compact disk or sent over the Internet, and yet the quality or content of the message has not changed by changing the means of conveying it.

As George Williams puts it: "The gene is a package of information, not an object. The pattern of base pairs in a DNA molecule specifies the gene. But the DNA molecule is the medium, it's not the message" (quoted by Johnson, p. 70).

Information from an intelligent source

In addition, this type of high-level information has been found to originate only from an intelligent source.

As Lee Strobel explains: "The data at the core of life is not disorganized, it's not simply orderly like salt crystals, but it's complex and specific information that can accomplish a bewildering task—the building of biological machines that far outstrip human technological capabilities" (p. 244).

For instance, the precision of this genetic language is such that the average mistake that is not caught turns out to be one error per 10 billion letters. If a mistake occurs in one of the most significant parts of the code, which is in the genes, it can cause a disease such as sickle-cell anemia. Yet even the best and most intelligent typist in the world couldn't come close to making only one mistake per 10 billion letters—far from it.

So to believe that the genetic code gradually evolved in Darwinian style would break all the known rules of how matter, energy and the laws of nature work. In fact, there has not been found in nature any example of one information system inside the cell gradually evolving into another functional information program.

Michael Behe, a biochemist and professor at Pennsylvania's Lehigh University, explains that genetic information is primarily an instruction manual and gives some examples.

He writes: "Consider a step-by-step list of [genetic] instructions. A mutation is a change in one of the lines of instructions. So instead of saying, "Take a 1/4-inch nut," a mutation might say, "Take a 3/8-inch nut." Or instead of "Place the round peg in the round hole," we might get "Place the round peg in the square hole" . . . What a mutation cannot do is change all the instructions in one step—say, [providing instructions] to build a fax machine instead of a radio" (Darwin's Black Box, 1996, p. 41).

We therefore have in the genetic code an immensely complex instruction manual that has been majestically designed by a more intelligent source than human beings.

Even one of the discoverers of the genetic code, the agnostic and recently deceased Francis Crick, after decades of work on deciphering it, admitted that "an honest man, armed with all the knowledge available to us now, could only state that in some sense, the origin of life appears at the moment to be almost a miracle, so many are the conditions which would have had to have been satisfied to get it going" (Life Itself, 1981, p. 88, emphasis added).

Evolution fails to provide answers

It is good to remember that, in spite of all the efforts of all the scientific laboratories around the world working over many decades, they have not been able to produce so much as a single human hair. How much more difficult is it to produce an entire body consisting of some 100 trillion cells!

Up to now, Darwinian evolutionists could try to counter their detractors with some possible explanations for the complexity of life. But now they have to face the information dilemma: How can meaningful, precise information be created by accident—by mutation and natural selection? None of these contain the mechanism of intelligence, a requirement for creating complex information such as that found in the genetic code.

Darwinian evolution is still taught in most schools as though it were fact. But it is increasingly being found wanting by a growing number of scientists. "As recently as twenty-five years ago," says former atheist Patrick Glynn, "a reasonable person weighing the purely scientific evidence on the issue would likely have come down on the side of skepticism [regarding a Creator]. That is no longer the case." He adds: "Today the concrete data point strongly in the direction of the God hypothesis. It is the simplest and most obvious solution . . ." (God: The Evidence, 1997, pp. 54-55, 53).

Quality of genetic information the same

Evolution tells us that through chance mutations and natural selection, living things evolve. Yet to evolve means to gradually change certain aspects of some living thing until it becomes another type of creature, and this can only be done by changing the genetic information.

So what do we find about the genetic code? The same basic quality of information exists in a humble bacteria or a plant as in a person. A bacterium has a shorter genetic code, but qualitatively it gives instructions as precisely and exquisitely as that of a human being. We find the same prerequisites of a language—alphabet, grammar and semantics—in simple bacteria and algae as in man.

Each cell with genetic information, from bacteria to man, according to molecular biologist Michael Denton, consists of "artificial languages and their decoding systems, memory banks for information storage and retrieval, elegant control systems regulating the automated assembly of parts and components, error fail-safe and proof-reading devices utilized for quality control, assembly processes involving the principle of prefabrication and modular construction . . . [and a] capacity not equalled in any of our most advanced machines, for it would be capable of replicating its entire structure within a matter of a few hours" (Denton, p. 329).

So how could the genetic information of bacteria gradually evolve into information for another type of being, when only one or a few minor mistakes in the millions of letters in that bacterium's DNA can kill it?

Again, evolutionists are uncharacteristically silent on the subject. They don't even have a working hypothesis about it. Lee Strobel writes: "The six feet of DNA coiled inside every one of our body's one hundred trillion cells contains a four-letter chemical alphabet that spells out precise assembly instructions for all the proteins from which our bodies are made . . . No hypothesis has come close to explaining how information got into biological matter by naturalistic means" (Strobel, p. 282).

Werner Gitt, professor of information systems, puts it succinctly: "The basic flaw of all evolutionary views is the origin of the information in living beings. It has never been shown that a coding system and semantic information could originate by itself [through matter] . . . The information theorems predict that this will never be possible. A purely material origin of life is thus [ruled out]" (Gitt, p. 124).

The clincher

Besides all the evidence we have covered for the intelligent design of DNA information, there is still one amazing fact remaining—the ideal number of genetic letters in the DNA code for storage and translation.

Moreover, the copying mechanism of DNA, to meet maximum effectiveness, requires the number of letters in each word to be an even number. Of all possible mathematical combinations, the ideal number for storage and transcription has been calculated to be four letters.

This is exactly what has been found in the genes of every living thing on earth—a four-letter digital code. As Werner Gitt states: "The coding system used for living beings is optimal from an engineering standpoint. This fact strengthens the argument that it was a case of purposeful design rather that a [lucky] chance" (Gitt, p. 95).

More witnesses

Back in Darwin's day, when his book On the Origin of Species was published in 1859, life appeared much simpler. Viewed through the primitive microscopes of the day, the cell appeared to be but a simple blob of jelly or uncomplicated protoplasm. Now, almost 150 years later, that view has changed dramatically as science has discovered a virtual universe inside the cell.

"It was once expected," writes Professor Behe, "that the basis of life would be exceedingly simple. That expectation has been smashed. Vision, motion, and other biological functions have proven to be no less sophisticated than television cameras and automobiles. Science has made enormous progress in understanding how the chemistry of life works, but the elegance and complexity of biological systems at the molecular level have paralyzed science's attempt to explain their origins" (Behe, p. x).

Dr. Meyer considers the recent discoveries about DNA as the Achilles" heel of evolutionary theory. He observes: "Evolutionists are still trying to apply Darwin's nineteenth-century thinking to a twenty-first century reality, and it's not working ... I think the information revolution taking place in biology is sounding the death knell for Darwinism and chemical evolutionary theories" (quoted by Strobel, p. 243).

Dr. Meyer's conclusion? "I believe that the testimony of science supports theism. While there will always be points of tension or unresolved conflict, the major developments in science in the past five decades have been running in a strongly theistic direction" (ibid., p. 77).

Dean Kenyon, a biology professor who repudiated his earlier book on Darwinian evolution—mostly due to the discoveries of the information found in DNA—states: "This new realm of molecular genetics (is) where we see the most compelling evidence of design on the Earth" (ibid., p. 221).

Just recently, one of the world's most famous atheists, Professor Antony Flew, admitted he couldn't explain how DNA was created and developed through evolution. He now accepts the need for an intelligent source to have been involved in the making of the DNA code.

"What I think the DNA material has done is show that intelligence must have been involved in getting these extraordinary diverse elements together," he said (quoted by Richard Ostling, "Leading Atheist Now Believes in God," Associated Press report, Dec. 9, 2004).

"Fearfully and wonderfully made"

Although written thousands of years ago, King David's words about our marvelous human bodies still ring true. He wrote: "For You formed my inward parts, You covered me in my mother's womb. I will praise You, for I am fearfully and wonderfully made . . . My frame was not hidden from You, when I was made in secret, and skillfully wrought. . ." (Psalm 139:13-15, emphasis added).

Where does all this leave evolution? Michael Denton, an agnostic scientist, concludes: "Ultimately the Darwinian theory of evolution is no more nor less than the great cosmogenic myth of the twentieth century" (Denton, p. 358).

All of this has enormous implications for our society and culture. Professor Johnson makes this clear when he states: "Every history of the twentieth century lists three thinkers as preeminent in influence: Darwin, Marx and Freud. All three were regarded as 'scientific' (and hence far more reliable than anything 'religious') in their heyday.

"Yet Marx and Freud have fallen, and even their dwindling bands of followers no longer claim that their insights were based on any methodology remotely comparable to that of experimental science. I am convinced that Darwin is next on the block. His fall will be by far the mightiest of the three" (Johnson, p. 113).

Evolution has had its run for almost 150 years in the schools and universities and in the press. But now, with the discovery of what the DNA code is all about, the complexity of the cell, and the fact that information is something vastly different from matter and energy, evolution can no longer dodge the ultimate outcome. The evidence certainly points to a resounding checkmate for evolution! GN

[Ichneumon]

Evolutionists commonly like to snear that those that believe in a God are the "Flat Earth" society members.

Because there are a large number of parallels.

Rather it is the Evolutionist who still cling to the notion of "Spontaneous Generation" which was common in Darwins time.

Evolution is not at all the same thing as spontaneous generation -- do you really think that telling falsehoods helps your case any? Or were you just too ignorant to know the difference but spouted off about it anyway? Here, read this if you'd like to start your education so that you could start having an informed opinion instead of the usual propaganda-filled creationist type.

How anyone can look at the unfathomable complexity of living things, and believe that it occured through the mechanisms proposed by Darwin,

...because that's what the mountains of evidence and over a century of study overwhelmingly indicates.

requires a suspension of reason, and blind FAITH.

Complete and utter horse manure. You clearly don't have even the first clue about this subject, or the people who study it and understand it. Knowledge of the validity of evolution does not require "FAITH", blind or otherwise -- it requires knowledge, understanding, and a familiarity with the vast amounts of evidence and experimentation supporting it. It takes a deep knowledge of the processes involved and the pattern and history and structure and genetics of life. This is probably why most creationists are out in the cold when it comes to understanding evolution.

Here's an essay which refutes your fundamental mistake much better than I can:

Do You Believe in Evolution?
by Bob Riggins

Introduction

In my part of the country I get asked that a lot by students. That's partly because of the part of the country I'm in (South Texas). Fundamentalism-creationism is endemic around here, and somehow that noisy minority has convinced the indifferent majority that to be a Christian of any sort, one must reject evolution. Ironically, even many of my Catholic students think their church is "against evolution" (it isn't). Somehow Protestant fundamentalism has "converted" them, at least on this article of faith, without their even realizing it. Perhaps their own church has not strongly, positively, and publicly stated its position to parishioners.

Perhaps it's also because, as an English teacher in a science-oriented magnet school, I often include science fiction novels and, at least once a year, a science nonfiction book as assigned readings. Inevitably, there will be something (probably a lot of things) in those books that rub the creationists the wrong way, since to maintain their structure of beliefs they have had to reject the facts established in practically all areas of science, from astronomy through nuclear physics to geology and biochemistry. Perhaps they've actually never encountered a teacher who openly "believes in" evolution (a very real possibility around here). Now that's scary! No wonder on those international comparisons our students score worse than kids in Lower Slobovia or wherever.

The Question

But the problem I want to deal with here is how to answer that question: Do you believe in evolution? It's easy to say "Yes!" but that's not right. The problem is that the question itself is wrong. It's like the old "Have you stopped beating your wife?" question: either a yes or a no gives the wrong impression.

I certainly don't want to say no, since that would create an entirely wrong impression. But answering yes isn't quite right, either. The problem is the phrase "believe in," just as the "have you stopped" is the trap in the earlier example.

Concentrate on the believe in: no, I don't believe in evolution. Think of how that phrase is often applied. Little kids believe in Santa Claus and the Easter Bunny. We often judge their maturity by finding out which things they still believe in and which they have "grown out of" ("Aren't you a little old to still believe in the Tooth Fairy?"). The phrase believe in in common parlance seems to mean to take something literally for which there is little or no objective evidence. You must believe in the Easter Bunny, because you've never seen the real one yourself, there's nothing he has done that couldn't be simply explained by ordinary phenomena (parental trickery), and there's no objective, physical, replicable (in other words, scientific) evidence that he's real. If you had those last things, then you wouldn't have to believe in the Easter Bunny, you would know he was real.

Knowing vs. Believing

That's the difference: you absolutely know some things are real, through your own experience or other kinds of really solid proof. That's knowledge, not belief. Other things you believe in. You want them to be true. It would be nice if they were true. It's probably fun to believe in them. But you don't have solid, irrefutable (scientific) proof, so you have to keep believing in them, rather than knowing them (or you could just throw them out entirely, like most of us over six have done with Santa Claus). If you had that kind of evidence, then the folks whose job it is to find out the physical facts about the world (scientists) would know them too, and belief wouldn't be required. A mark of the immaturity of small children is that they haven't learned this distinction yet. About the only proof they may demand is what someone older tells them, or what they see on TV. Note also that you can't trust the believer. He may, of course, say he "knows" his favorite belief is true, and may trot out what to him is adequate proof ("But I saw Santa in the store, and look at all the stuff he brought, and on the news they saw him on the radar, and... and..."). Or he may be one of those incredibly shallow people whose answer amounts to, "I don't know why, I just believe it," or the ludicrous contradiction, "I just know it's true."

There's another common meaning for "believe in," as in "Do you believe in democracy?" "Do you believe in the American Dream?" "Do you believe in abortion under certain circumstances?" "Do you believe in the justice of our cause?" Here the meaning of "believe in" seems to be something like "trust," or "think it's probably best," or "are willing to go along with." That doesn't seem to be what someone is getting at when he asks me if I believe in evolution, or at least that's not how I take the question. So in that sense, no, I don't believe in evolution: it's not a matter of personal opinion, or philosophy, or a gray area where one must decide what might be best overall.

But back to the real distinction: no, I don't believe in evolution--I know that it's real. It doesn't require believing in. And I don't "just know it," like the vacuous air-head. I have all the objective evidence I need for real knowledge . The reality of evolution having occurred and continuing to occur is every bit as strongly established as the knowledge that the Earth is round, that germs cause disease, that electrons exist, or that the speed of light is ~300,000 kilometers/second. If anything, I have more daily-life experience to show me evolution happening than I have for those other things. I can see that offspring aren't identical to their parents. I have seen new varieties of plants and animals developed within my own lifetime. I live in an area where boll weevils often win the evolutionary race to develop resistance to pesticides. I can easily catch a case of (newly evolved) resistant staphylococcus, which might very well kill me. I have seen and touched and personally found the fossils of the now-extinct ancestors of living creatures.

Evidence of Evolution Is Stronger Than Evidence of Electrons

As a matter of fact, I have more down-to-earth proof of the reality of evolution than I have of the other things mentioned above, which I know to be real. I will never see an electron. How would I ever come close to accurately measuring the speed of light? My chances of ever getting far enough away from Earth to actually see for myself that it is round are practically nil; and I don't have the equipment or the expertise to ever really prove for myself that a particular breed of bacteria actually causes a particular disease. Then don't I just take those things "on faith"? Don't I believe in them, rather than actually knowing them? No. As a society, we have hired specialists to find out these kinds of things. We've done everything we can to assure that they are highly trained, that they are objective (not letting their philosophies or beliefs get in the way), that they are honest, and that their answers are true (they constantly check on each other, compete, and repeat experiments to make sure the results are real). We've set up a system (science) in which wrong answers are quickly thrown out, all answers are tested over and over in every imaginable way, right answers get righter all the time (e.g., relativity doesn't "disprove" Newtonian mechanics, it just improves on it; punctuated equilibrium doesn't "disprove" Darwinian evolution, it just clarifies it further), and the best way to make a name for yourself is to disprove an older idea (with enough proof of your own to stand up to the toughest tests). And finally, that system works far better than any other way mankind has ever tried for finding out about the physical world.

So what science knows, I know. They are my agents for finding out things I can't find out for myself. Science knows (and tells me) that there are electrons and what the speed of light is. I would be foolish to reject that knowledge. Science also tells me, with just as much assurance, that living things have evolved. I know that knowledge has been tested, tried, experimented with, and applied to real situations, and has proven its "fitness" by growing stronger through 150 years of severe testing. I would be foolish to reject that knowledge.

So no, I don't believe in evolution; I know that it has happened and still does. As a matter of fact, I should probably feel insulted. If you asked me if I believe the Earth is round, that would be insulting. Do you think I could be so ignorant as to believe it is flat? The same goes for evolution. Do you think I would reject the last two centuries of scientific progress and the evidence of my own eyes? I should be thoroughly offended.

[Pan_Yan]

Christians can always celebrate Christmas.

Jews can celebrate Hanukkah.

Muslims can celebrate Ramadan.

Race baiters can celebrate Quanza.

Evolutionists can celebrate multicultural diversity giving tree winter solstice day.


The difference is Christians must be shunned for their celebration.

[Ichneumon]

Dr. Behe spoke in Ithaca this past week, and reiterated - by citing writings of prominent Darwinists themselves - that no one has yet demonstrated how any complex biochemical systems have "happened to develop" in the incremental stepwise manner that classical Darwinism requires.

Behe has been repeating this lie for years, but it's still a lie (or a bit of grossly incompetent ignorance on his part, but I'd rather give him the benefit of the doubt).

Publish or Perish

Some Published works on Biochemical Evolution

edited by John Catalano

Copyright © 1998-2004
[Text updated: October 16, 2001]
[Links updated: January 25, 2004]

Other Links:
Outside links open in new windows

The Elusive Scientific Basis of Intelligent Design Theory

So-called "intelligent design theory," of which Behe is a major proponent, has produced no publications in major scientific journals. Who was it that said publish or perish?

Behe's Empty Box

This web page contains many links to web pages supporting or criticizing Behe's work.

Irreducible Complexity and the Evolutionary Literature: Response to Critics

This article includes Behe's response to this page.

n page 179 of Darwin's Black Box Michael Behe claims:

"There has never been a meeting, or a book, or a paper on details of the evolution of complex biochemical systems."

He closes the chapter with this ludicrous statement:

"In effect, the theory of Darwinian molecular evolution has not published, and so it should perish"

(Did someone say publish or perish?: The Elusive Scientific Basis of Intelligent Design Theory)

To be honest, I suspect that the extent of detail Behe is demanding would require a combination cutting-edge biochemistry lab and a time machine. How else can science fully recover, for example, every single step in the evolution of the bacterial flagellum that took place billions of years ago?

In any case the claim itself is false since papers do in fact exist that attempt to flesh out the details of the evolution of various biochemical systems and structures. Many such citations are included below.

But that is only part of the story. There are thousands of additional published papers containing solid and detailed evidence of biochemical evolution:

• Evidence of gene duplications and subsequent functional divergence, or functional loss in the form of pseudogenes.
• Evidence of exon shuffling and modular re-use within proteins.
• Evidence of both natural selection and neutral drift at the molecular level.
• Evidence of the malleable and adaptive nature of molecular evolution itself. For example in recent shocking cases of bacterial drug resistance - the evolution of evolvability.
• Evidence that the phylogeny inferred from protein and DNA sequence comparisons is correlated with the phylogeny inferred from evolutionary biology.
• Evidence that within every studied biochemical system, the "parts" themselves have evolved, and the interactions between those parts have also evolved. Are we to believe that an intelligent designer builds with components that evolve via the blind forces of mutation, selection and drift?

Most of the citations and abstracts below were found using the PubMed MEDLINE search engine and microbiology database. A simple search reveals that there are over 13,000 articles that contain "evolution" as a major subject keyword - hardly the dead silence that Behe proclaims. Granted many of these do not directly address the problem of adaptive complexity in biochemical systems, but many of them do.

Note that I have excluded papers that discuss sequence comparisons being used solely to determine lines of descent. Michael Behe already admits that common descent is reasonable.

Keep in mind this is only a small sampling of citations collected from my own searches, and from the suggestion of others (thanks for those suggestions!)

Last but not least. Please help me find more citations and continue to grow this page - especially if you have a background in biochemistry or microbiology. Thank you.

---

Introduction

• + Molecular Evolution - brief summary with definition

Books

• Cells, Embryos, And Evolution: Towards a Cellular and Developmental Understanding of Phenotypic Variation and Evolutionary Adaptability - a recent textbook by John Gerhart and Marc Kirschner (1997 Blackwell Science) - "In writing Cells, Embryos, and Evolution, our aim has been to continue what Darwin started: to understand not only the influence of selection on the path of evolution, but also the capacity of the organism to generate heritable variation upon which selection can act."
  Preface / amazon.com bookstore
• Four Billion Years An Essay on the Evolution of Genes and Organisms by Willam F. Loomis
• Vital Dust : Life As a Cosmic Imperativeby Christian De Duve
• Many of these books suggested by David Ussery, Ph.D (thanks!):
• +Molecular Strategies in Biological Evolution - Proceedings of a New York Academy of
  Sciences conference, June 27-29, 1998. Lynn Helena Caporale, Editor.
• + Molecular Approaches to Ecology and Evolution by by Rob Desalle (Editor), B. Schierwater (Editor)  (98)
• + Molecular Evolution by Wen-Hsiung Li (97)
• + Patterns in Evolution: The New Molecular View by Roger Lewin (96)
• + Chemical Evolution: Physics of the Origin and Evolution of Life (96)
• + Tracing Biological Evolution in Protein and Gene Structures (96)
• + Molecular Evolution (Biomathematics V. 24) by Vadim Aleksandrovich Ratner (Editor) (96)
• +GENE FAMILIES STRUCTURE FUNCTION GENETICS AND EVOLUTION Proceedings of the VIII International Congress on Isozymes (95)
• + Genetics and Evolution The Molecules of Inheritance (New Encyclopedia of Science) (95)
• + The Causes of Molecular Evolution (94)
• + The Origins of Order Self-Organization and Selection in Evolution by Stuart A. Kauffman (92)
• + Molecular Evolution of the Major Histocompatibility Complex (92)
• + Molecular Evolution on Rugged Landscapes; Proteins RNA and the Immune System by Stuart A. Kauffman (91)
• + Evolution at the Molecular Level  by Robert K. Selander, Andrew G. Clark, Thomas S. Whittam (Editor) (91)
• + Evolution of Life: Fossils Molecules and Culture by S. Osawa, T. Honjo (Editor) (91)
• + Molecular Theory of Evolution (85)
• + Multidomain Proteins Structure and Evolution
• +Evolutionary Design by Computers edited by Peter J. Bentley. Book & CD-ROM edition (May 1999) Amazon.com or Amazon.co.uk- Yes, evolution does produce irreducible complexity!
  • Author's Book Page with related links, Author's home page, More Ordering Information
• + Search for Life on Mars by Malcolm Walter, 1999 - contains origins of life scenarios

Conferences

• + Do Genomes Enhance Their Own Evolution? - "At a conference on molecular strategies in biological evolution, researchers discussed how evolutionary strategies can evolve, making the process of evolution more efficient."
• + New Passion for Evo-Devo - Fifth Annual Meeting of the Society for Molecular Biology and Evolution

Immune System

• +The Evolution of Improved Fitness by random mutation plus selection by Edward E. Max, M.D., Ph.D. [Talk.Origins archive] Michael Behe likes to talk about the human immune system, but what lessons should we really learn from such a system?
• Immunity and the Invertebrates - "the fabulously complex immune systems of humans and other mammals evolved over hundreds of millions of years - in sometimes surprising ways. Scientific American Nov 1996
• Sharks and the Origins of Vertebrate Immunity. Scientific American Nov 1996
• + Ancient Jumping DNA May Have Evolved Into Key Component Of Human Immune System
• + Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system
• Evolution of immune reactions - "The history and evolutionary pathways of defense reactions among various forms of life are reconstructed"
• New insights into V(D)J recombination and its role in the evolution of the immune system - no abstract avail
• Evolution and developmental regulation of the major histocompatibility complex
• Evolution of the IL-6/class IB cytokine receptor family in the immune and nervous systems - "we speculate on a plausible molecular pathway"
• Layered evolution in the immune system. A model for the ontogeny and development of multiple lymphocyte lineages - no abstract avail
• Development of an immune system
• The ancestor of the adaptive immune system was the CAM system for organogenesis
• The evolutionary origins of immunoglobulins and T-cell receptors: possibilities and probabilities - no abstract avail
• Evolutionary perspectives on amyloid and inflammatory features of Alzheimer disease
• Organization of the human RH50A gene (RHAG) and evolution of base composition of the RH gene family.
• Molecular evolution of the vertebrate immune system.
• Morphostasis: an evolving perspective.
• Rapid evolution of immunoglobulin superfamily C2 domains expressed in immune system cells.

Blood Coagulation

• Reconstructing the evolution of vertebrate blood coagulation from a consideration of the amino acid sequences of clotting proteins - no, this is not the "ying and yang" presentation from Behe's book
• Evolutionary assembly of blood coagulation proteins - no abstract avail
• Exon and domain evolution in the proenzymes of blood coagulation and fibrinolysis - no abstract avail
• Evolution of proteolytic enzymes
• Evolution of vertebrate fibrin formation and the process of its dissolution.

Globin

• + Common Parasite Overturns Traditional Beliefs About The Evolution And Role Of Hemoglobin - "reveals that hemoglobin evolved first and foremost to handle the molecule nitric oxide (NO) rather than oxygen"
• + Scientists Discover How Bacteria Protect Themselves Against Immune System - "So we are now providing an understanding of the evolutionary basis of hemoglobin and the original function of the hemoglobin family - to detoxify nitric oxide."
• + The Evolution of Hemoglobin by Ross Hardison, (Abstract) American Scientist, March-April 1999
• Globins in nonvertebrate species: dispersal by horizontal gene transfer and evolution of the structure-function relationships
• Reduction of two functional gamma-globin genes to one: an evolutionary trend in New World monkeys
• Evolutionary history of introns in a multidomain globin gene
• Hemoglobin A2: origin, evolution, and aftermath - no abstract avail

Flagella and Cilium

• Early evolution of microtubules and undulipodia
• Flagellar beat patterns and their possible evolution - "The most sophisticated flagellar mechanisms are best explained as having been evolved for the collection of particulate food"
• A temporary flagellate (mastigote) stage in the vahlkampfiid amoeba Willaertia magna and its possible evolutionary significance
• The evolutionary origin and phylogeny of eukaryote flagella - no abstract avail
• + Molecular analysis of archael flagellins: similarity to the type IV pilin-transport superfamily widespread in bacteria
• Molecular evolution of the C-terminal cytoplasmic domain of a superfamily of bacterial receptors involved in taxis - "The gene coding for the C-terminal cytoplasmic domain of these proteins apparently evolved through gene duplication from a common ancestor"
• Dynein family of motor proteins: present status and future questions - evolution of Dynein via gene duplication
• Origins of the nucleate organisms - "The phylogeny supports the hypotheses that the flagellum developed from the spindle system"
• The evolutionary origin and phylogeny of microtubules, mitotic spindles and eukaryote flagella - no abstract avail
• The evolution of cellular movement in eukaryotes: the role of microfilaments and microtubules - no abstract avail

Other Motor Proteins

• +Kinesin Motor Phylogenetic Tree - Behe likes to play down the importance of sequence comparisons. It's no wonder - just click around this diagram for a while. It becomes obvious that an important motor protein like kinesin has gradually evolved across many species. From the Kinesin HomePage.

Actin

• Evolution of a dynamic cytoskeleton
• Isolation, characterization and evolution of nine pufferfish (Fugu rubripes) actin genes
• Evolution of chordate actin genes: evidence from genomic organization and amino acid sequences
• Structural comparisons of muscle and nonmuscle actins give insights into the evolution of their functional differences

Cell Membrane - Receptors, Pumps, etc.

• + Molecular evolution of glutamate receptors: a primitive signaling mechanism that existed before plants and animals diverged.
• Co-evolution of ligand-receptor pairs in the vasopressin/oxytocin superfamily of bioactive peptides
• The evolution of the synapses in the vertebrate central nervous system
• Evolutionary origins of multidrug and drug-specific efflux pumps in bacteria.
• A comprehensive evolutionary analysis based on nucleotide and amino acid sequences of the alpha- and beta-subunits of glycoprotein hormone gene family.

Citric Acid Cycle (Krebs Cycle)

• The puzzle of the Krebs citric acid cycle: assembling the pieces of chemically feasible reactions, and opportunism in the design of metabolic pathways during evolution
• The evolution of metabolic cycles
• Evolution of the first metabolic cycles
• Chemical evolution of the citric acid cycle: sunlight photolysis of the amino acids glutamate and aspartate
• Speculations on the origin and evolution of metabolism
• The Molecular Anatomy of an Ancient Adaptive Eventby Anthony M. Dean (American Scientist Jan-Feb 1998) - "Using a combination of the modern techniques of structural biochemistry and protein engineering, combined with molecular phylogeny, the author recreates the story of this very ancient event."

Amino Acid Biosynthesis

• New prospects for deducing the evolutionary history of metabolic pathways in prokaryotes: aromatic biosynthesis as a case-in-point
• Biochemical pathways in prokaryotes can be traced backward through evolutionary time
• Enzyme specialization during the evolution of amino acid biosynthetic pathways
• Enzyme recruitment in evolution of new function

Gylcolysis

• Evolution of glycolysis - no abstract available
• Bioenergetics: the evolution of molecular mechanisms and the development of bioenergetic concepts
• Theoretical approaches to the evolutionary optimization of glycolysis--chemical analysis
• The evolution of kinetoplastid glycosomes

Photosynthesis

• Stepwise molecular evolution of bacterial photosynthetic energy conversion
• Evolution of photosynthetic reaction centers and light harvesting chlorophyll proteins
• Evolution of photosynthetic reaction centers
• Early evolution of photosynthesis: clues from nitrogenase and chlorophyll iron proteins
• Evolution of the control of pigment and plastid development in photosynthetic organisms
• Chemical evolution of photosynthesis

Lysozome

• Molecular evolution of ruminant lysozymes
• Adaptive evolution of lysozyme: changes in amino acid sequence, regulation
  of expression and gene number
• Evolution of stomach lysozyme: the pig lysozyme gene

Vision

• + The evolution of trichromatic color vision by opsin gene duplication in New World and Old World primates
• The Evolution of Color Vision - byMickey Rowe from the Talk.Origins archive.
• Molecular basis for tetrachromatic color vision - rhodopsins diverged from cone-type pigment
• Molecular evolution of the Rh3 gene in Drosophila
• Interphotoreceptor retinoid-binding protein. Gene characterization, protein repeat structure, and its evolution
• Spectral tuning and molecular evolution of rod visual pigments in the species flock of cottoid fish in Lake Baikal
• The evolution of rhodopsins and neurotransmitter receptors - another example of the importance of sequence comparisons in studying evolution. Behe dismisses comparisons as a limited tool in determining lines of descent.
• Optimization, constraint, and history in the evolution of eyes
• A pessimistic estimate of the time required for an eye to evolve - remember the last claim to irredicible complexity?
• Sequence analysis of teleost retina-specific lactate dehydrogenase C: evolutionary implications for the vertebrate lactate dehydrogenase gene family
• The eye of the blind mole rat (Spalax ehrenbergi): regressive evolution at the molecular level - no abstract avail
• The evolution of eyes. - "...The presence of homologous constituent molecules in nonhomologous structures reminds us that molecules are not eyes."
  

Development

• + Programming the Drosophila embryo
• + Evolution of chordate hox gene clusters
• + Hox genes in brachiopods and priapulids and protostome evolution.
• +Radical evolutionary change possible in a few generations
• + Evolution Re-Sculpted Animal Limbs By Genetic Switches Once Thought Too Drastic For Survival - "Today's finding marks the first time that changes in the control of homeotic genes have been shown to underlie an evolutionary trend leading to novel body structures." (also here: Animal Limb Evolution)
• + Flatworms Are Oldest Living Ancestors To Those Of Us With Right And Left Sides Researchers Report In Science
• The origin and evolution of animal appendages
• Hox genes in evolution: protein surfaces and paralog groups
• Evolution of the insect body plan as revealed by the Sex combs reduced expression pattern
• Sea urchin Hox genes: insights into the ancestral Hox cluster
• Theoretical approaches to the analysis of homeobox gene evolution
• Teleost HoxD and HoxA genes: comparison with tetrapods and functional evolution of the HOXD complex
• Evolutionary origin of insect wings from ancestral gills
• Tracing backbone evolution through a tunicate's lost tail
• Classification and phylogeny of the MADS-box multigene family suggest defined roles of MADS-box gene subfamilies in the morphological evolution of eukaryotes
• Modification of expression and cis-regulation of Hoxc8 in the evolution of diverged axial morphology.
• The ParaHox gene cluster is an evolutionary sister of the Hox gene cluster.

Transcription / Translation / Duplication

• Gene duplications in evolution of archaeal family B DNA polymerases
• Adaptive amino acid replacements accompanied by domain fusion in reverse transcriptase
• Molecular evolution of genes encoding ribonucleases in ruminant species
• Studies on the sites expressing evolutionary changes in the structure of eukaryotic 5S ribosomal RNA
• Evolution of a Transfer RNA Gene Through a Point Mutation in the Anticodon
• Archaeal translation initiation revisited: the initiation factor 2 and eukaryotic initiation factor 2B alpha-beta-delta subunit families
• Universally conserved translation initiation factors
• Genetic code in evolution: switching species-specific aminoacylation with a peptide transplant.
• Evolution of transcriptional regulatory elements within the promoter of a mammalian gene.
• Codon reassignment and amino acid composition in hemichordate mitochondria.

From Russell F. Doolittle

• Reconstructing the evolution of vertebrate blood coagulation from a consideration of the amino acid sequences of clotting proteins - no, this is not the "ying and yang" presentation from Behe's book
• Determining divergence times of the major kingdoms of living organisms with a protein clock - At least Behe thinks that common descent is "reasonable".
• The multiplicity of domains in proteins - evolution via domain shuffling
• Characterization, primary structure, and evolution of lamprey plasma albumin - protein evolution via gene duplication
• The origins and evolution of eukaryotic proteins
• Evolution of vertebrate fibrin formation and the process of its dissolution.

Drug resistance is biochemical evolution

• +HIV Mutating Too Fast For Drug Cocktail - "Because of HIV's high mutation rate, it provides a unique opportunity to study the processes of evolution,"
• The Challenge of Antibiotic Resistance. SciAm, March 98

Other

• + Vastly Different Virus Families May Be Related
• + Selective sweep of a newly evolved sperm-specific gene in Drosophila
• + Activated acetic acid by carbon fixation on (Fe,Ni)S under primordial conditions
• Molecular evolution of the histidine biosynthetic pathway
• Accelerated evolution in inhibitor domains of porcine elafin family members
• Tandem arrangement of the human serum albumin multigene family in the sub-centromeric region of 4q: evolution and chromosomal direction of transcription
• The B12-dependent ribonucleotide reductase from the archaebacterium Thermoplasma acidophila: an evolutionary solution to the ribonucleotide reductase conundrum
• Ancient divergence of long and short isoforms of adenylate kinase: molecular evolution of the nucleoside monophosphate kinase family
• Convergent evolution of antifreeze glycoproteins in Antarctic notothenioid fish and Arctic cod
• + Evolution of antifreeze glycoprotein gene from a trypsinogen gene in Antarctic notothenioid fish - "We have found that the antifreeze glycoproteins (AFGPs) of the predominant Antarctic fish taxon, the notothenioids, evolved from a pancreatic trypsinogen. We have determined the likely evolutionary process..."
• + Evolution of an antifreeze glycoprotein (no abstract)
• A model for the evolution of the plastid sec apparatus inferred from secY gene phylogeny
• The evolutionary history of the amylase multigene family in Drosophila pseudoobscura
• Accelerated evolution of Trimeresurus okinavensis venom gland phospholipase A2 isozyme-encoding genes
• The evolution of an allosteric site in phosphorylase
• Molecular evolution of fish neurohypophysial hormones: neutral and selective evolutionary mechanisms
• Pseudogenes in ribonuclease evolution: a source of new biomacromolecular function?
• Evolution of hemopoietic ligands and their receptors. Influence of positive selection on correlated replacements throughout ligand and receptor proteins
• Evolutionary relationships of the carbamoylphosphate synthetase genes
• The molecular evolution of the small heat-shock proteins in plants
• Phylogenetic analysis of carbamoylphosphate synthetase genes: complex evolutionary history includes an internal duplication within a gene which can root the tree of life
• Duplication and functional divergence in the chalcone synthase gene family of Asteraceae: evolution with substrate change and catalytic simplification
• Evolutionary history of the 11p15 human mucin gene family.
• Molecular evolution of the aldo-keto reductase gene superfamily.
• Molecular evolution allows bypass of the requirement for activation loop phosphorylation of the Cdc28 cyclin-dependent kinase.

General

• +A Classification of Possible Routes of Darwinian Evolution by Richard T. Thornhill and David W. Ussery, Journal of Theoretical Biology, 203:111-116, 2000 -  "...This classification provides a conceptual framework within which to investigate the accessibility by Darwinian evolution of complex biological structures." (For the record, I don't agree with their conclusion that Orr's proposed route can not produce irreducible complexity - John C)
• + Generation of evolutionary novelty by functional shift+Evolutionary Insights Stem From Sloppy Copy Discovery
• + Mobile DNA Sequences Could Be The Cause Of Chromosomal Mutations During The Evolution Of Species
• + A domain model for eukaryotic DNA organization: a molecular basis for cell differentiation and chromosome evolution.
• + The domain model for eukaryotic DNA organization. 2: A molecular basis for constraints on development and evolution.
• +Minor Shuffle Makes Protein Fold - "the finding makes the evolution of new protein shapes easier to understand, because it implies that proteins can adapt through small changes and preserve some structural elements while discarding others."
• + Genetic Stowaways May Contribute To Evolutionary Change
• +Evolutionary Molecular Mechanism In Mammals Found
• +Complete Genomes - "This page contains the results of in-depth analysis of complete genome sequences of cellular life forms"
• Genetic redundancy caused by gene duplications and its evolution in networks of transcriptional regulators
• Strong evolutionary conservation of broadly expressed protein isoforms in the troponin I gene family and other vertebrate gene families
• Cases of ancient mobile element DNA insertions that now affect gene regulation
• Punctuated evolution caused by selection of rare beneficial mutations
• The origin of programmed cell death - no abstract avail
• The origin and early development of biological catalysts
• DNA secondary structures and the evolution of hypervariable tandem arrays
• Episodic adaptive evolution of primate lysozymes - testing for adaptation
• Genome plasticity as a paradigm of eubacteria evolution
• Evolutionary motif and its biological and structural significance
• Neutral and nonneutral mutations: the creative mix--evolution of complexity in gene interaction systems
• Exon shuffling and other ways of module exchange and Domain organizations of modular extracellular matrix proteins and their evolution
• Introns and gene evolution
• New Drosophila introns originate by duplication.
• Evolution and the structural domains of proteins
• The role of constrained self-organization in genome structural evolution
• A possible origin of newly-born bacterial genes: significance of GC-rich nonstop frame on antisense strand
• The coevolution of gene family trees
• The evolution of metabolic cycles
• The emergence of major cellular processes in evolution
• A hardware interpretation of the evolution of the genetic code - "A quantitative rationale for the evolution of the genetic code is developed considering the principle of minimal hardware" - note that "minimizing hardware" is one plausible path to evolving "irreducibly complex" systems.
• Speculations on the origin and evolution of metabolism
• Probabilistic reconstruction of ancestral protein sequences and Search for ancient patterns in protein sequences
• The contribution of slippage-like processes to genome evolution
• Molecular evolution in bacteria
• The structural basis of molecular adaptation.

Someone say Intelligent?

• Mitochondrial DNA: molecular fossils in the nucleus
• Cases of ancient mobile element DNA insertions that now affect gene regulation
• Tiggers and DNA transposon fossils in the human genome
• The eye of the blind mole rat (Spalax ehrenbergi): regressive evolution at the molecular level - no abstract avail
• Tiggers and DNA transposon fossils in the human genome

Cancer as Molecular Evolution

• Gene competition and the possible evolutionary role of tumours

Test Tube and Artificial Evolution

• + New Scientist Planet Science: Replaying life -At last, we can watch evolution happen over and over again in the microworlds of the lab. And in playing God, we are laying bare the very forces that shape all living things, says Kate Douglas
• Molecular evolution of an arsenate detoxification pathway by DNA shuffling - "These results show that DNA shuffling can improve the function of pathways by complex and unexpected mutational mechanisms that may be activated by point mutation. These mechanisms may be difficult to explain and are likely to be overlooked by rational design"
• UB Researcher Developing Method That Employs Evolution To Develop New Drug Leads
• Directed evolution of a type I antifreeze protein expressed in Escherichia coli with sodium chloride as selective pressure and its effect on antifreeze tolerance
• Directed evolution of biosynthetic pathways. Recruitment of cysteine thioethers for constructing the cell wall of Escherichia coli
• Exploring the functional robustness of an enzyme by in vitro evolution
• Evolutionary algorithms in computer-aided molecular design
• Mutations to the Rescue - unintelligent design
• + Researchers Engineer A Way To Improve T-Cell Receptors - using Darwinian selection
• + Digital Organisms Give Life To Questions Of Evolution (The Avida Artificial Life Group Home Page)

Origin of Life and Cells

• +Good intro: Lies, Damned lies, Statistics, and Probability of Abiogenesis Calculations
• +Purdue Study Breathes New Life Into Question Of How Life Began - self-replicating peptides
• + Ammonia From The Earth's Deep Oceans A Key Step In The Search For Life's Origins
• + Whitehead Study Supports Existence Of Ancient RNA World Helps Provide Insight Into Early Evolution Of Life
• + Yale Scientists Recreate Molecular Fossils Now Extinct That May Have Existed At The Beginning Of Life
• +A whole old world - new evidence for "The RNA World"
• The path from the RNA world.
• Relics from the RNA world.
• A supersymmetric model for the evolution of the genetic code.
• The hydrogen hypothesis for the first eukaryote.
• + Kick-start for life on earth
• The Beginnings of Life on Earth by Christian de Duve
• +Are the Odds Against the Origin of Life Too Great to Accept? : Addenda to Review of David Foster's The Philosophical Scientists by Richard C. Carrier. From Bad Science Worse Philosophy the Quackery and Logic-Chopping of David Foster's The Philosophical Scientists

More Visitor Submissions(thanks!)

Here are a number of articles from a quick search of the Journal of Biological Chemistry using the word "evolution" at http://www.jbc.org/ --

Andrew P. Spicer and John A. McDonald Characterization and Molecular Evolution of a Vertebrate Hyaluronan Synthase Gene Family J. Biol. Chem. 1998 273: 1923-1932.

Catherine TomHon, Wei Zhu, David Millinoff, Kenji Hayasaka, Jerry L. Slightom, Morris Goodman, and Deborah L. Gumucio Evolution of a Fetal Expression Pattern via cis Changes near the Globin Gene J. Biol. Chem. 1997 272: 14062-14066.

Chien-Chia Wang, Andrey Pavlov, and Jim D. Karam Evolution of RNA-binding Specificity in T4 DNA Polymerase J. Biol. Chem. 1997 272: 17703-17710.

David R. Gang, Hiroyuki Kasahara, Zhi-Qiang Xia, Kristine Vander Mijnsbrugge, Guy Bauw, Wout Boerjan, Marc Van Montagu, Laurence B.Davin, and Norman G. Lewis Evolution of Plant Defense Mechanisms. RELATIONSHIPS OF PHENYLCOUMARAN BENZYLIC ETHER REDUCTASES TO PINORESINOL-LARICIRESINOL AND ISOFLAVONE REDUCTASES J. Biol. Chem. 1999 274: 7516-7527.

Elizabeth A. Bucher, Gurtej K. Dhoot, Mark M. Emerson, Margaret Ober, and Charles P. Emerson, Jr. Structure and Evolution of the Alternatively Spliced Fast Troponin T Isoform Gene J. Biol. Chem. 1999 274: 17661-17670.

Florence Magrangeas, Gilles Pitiot, Sigrid Dubois, Elisabeth Bragado-Nilsson, Michel ChŽrel, SŽverin Jobert, Benoit Lebeau, Olivier Boisteau, Bernard LethŽ, Jacques Mallet, Yannick Jacques, and StŽphane Minvielle Cotranscription and Intergenic Splicing of Human Galactose-1-phosphate Uridylyltransferase and Interleukin-11 Receptor -Chain Genes Generate a Fusion mRNA in Normal Cells. IMPLICATION FOR THE PRODUCTION OF MULTIDOMAIN PROTEINS DURING EVOLUTION J. Biol. Chem. 1998 273: 16005-16010.

James E. Hagstrom, Michael P. Fautsch, Monique Perdok, Anne Vrabel, and Eric D. Wieben Exons Lost and Found. UNUSUAL EVOLUTION OF A SEMINAL VESICLE TRANSGLUTAMINASE SUBSTRATE J. Biol. Chem. 1996271: 21114-21119. [

Juan Ausi— Histone H1 and Evolution of Sperm Nuclear Basic Proteins J. Biol. Chem. 1999 274: 31115-31118.

M. Neale Weitzmann, Kerry J. Woodford, and Karen Usdin DNA Secondary Structures and the Evolution of Hypervariable Tandem Arrays J. Biol. Chem. 1997 272: 9517-9523.

Marieta Costache, Pol-AndrŽ Apoil, Anne Cailleau, Anders Elmgren, Gšran Larson, Stephen Henry, Antoine Blancher, Dana Iordachescu, Rafael Oriol, and Rosella Mollicone Evolution of Fucosyltransferase Genes in Vertebrates J. Biol. Chem. 1997 272: 29721-29728.

Medeiros, Edward G. Rowan, Alan L. Harvey, and AndrŽ MŽnez On the Convergent Evolution of Animal Toxins. CONSERVATION OF A DIAD OF FUNCTIONAL RESIDUES IN POTASSIUM CHANNEL-BLOCKING TOXINS WITH UNRELATED STRUCTURES J. Biol. Chem. 1997 272: 4302-4309.

Ronald E. van Kesteren, Cornelis P. Tensen, August B. Smit, Jan van Minnen, Lee. F. Kolakowski, Jr., Wolfgang Meyerhof, Dietmar Richter, Harm van Heerikhuizen, Erno Vreugdenhil, and Wijnand P. M. Geraerts Co-evolution of Ligand-Receptor Pairs in the Vasopressin/Oxytocin Superfamily of Bioactive Peptides J. Biol. Chem. 1996 271: 3619-3626.

Sandra K. Parker and H. William Detrich III Evolution, Organization, and Expression of -Tubulin Genes in the Antarctic Fish Notothenia coriiceps. ADAPTIVE EXPANSION OF A GENE FAMILY BY RECENT GENE DUPLICATION, INVERSION, AND DIVERGENCE J. Biol. Chem. 1998 273: 34358-34369.

Stefanie Brumme, Volker Kruft, Udo K. Schmitz, and Hans-Peter Braun New Insights into the Co-evolution of Cytochrome c Reductase and the Mitochondrial Processing Peptidase J. Biol. Chem. 1998 273: 13143-13149.

Stephan M. MŸhlebach, Thomas Wirz, Urs BrŠndle, and Jean-Claude Perriard Evolution of the Creatine Kinases J. Biol. Chem. 1996 271: 11920-11929.

Zhe Lu, Elisa Cabiscol, Nuria Obradors, Jordi Tamarit, Joaquim Ros, Juan Aguilar, and E. C. C. Lin Evolution of an Escherichia coli Protein with Increased Resistance to Oxidative Stress J. Biol. Chem. 1998 273: 8308-8316.

(major MeSH 1998 Jan-May)

[Return to the Irreducible Complexity FAQs]

[Ichneumon]

Wouldn't it make MORE sense, to recognise that the case for intelligent creation is FAR stronger than Evolution.

It would make more sense if the ID case was actually "FAR stronger" than the case for evolution, but you have it exactly backwards, so no.

[weatherwax]

The whole problem with this debate is the assumption that there are only two possible answers, and one is correct. The assumptions states that either life arose and continues because of chance and biochemical reactions (for which there is no proof, and much against), or failing this, that life was created by an unkowable, mystic omniscient God (for which there is no proof, and much against).
The truth is that we are as much in the dark about the origins and continuance of life now as we have ever been. Molecular and sub-atomic science have given us sufficient knowledge to blow Darwin and his hangers-on out of the water. On the other hand, nothing has been discovered which demonstrates the presence of a mystical being.
So, we just dont know. Yet. Until the dogmatists in science give up on Evolution (which they never will while running scared from the label "creationist"), we will never add to our knowledge in order to find out.

[Centurion2000]

http://arxiv.org/abs/math-ph/0504033
http://arxiv.org/abs/quant-ph/0503203
http://arxiv.org/abs/nucl-th/0504015
http://arxiv.org/abs/quant-ph/0504193

Only one of those (3rd) appears to have any possible applications in engineering or materials work.

And hydrogen atoms are simple compared to DNA. You can spontaneously create hydrogen. Can you do the same with DNA ?

[Pan_Yan]

Believe in something ...

Believe in nothing ...

It's still belief ...

And I doubt very few people have had their beliefs changed while arguing on a thread.

[concerned about politics]

I think the scientific world itself will have to kill Darwinism because its own standards of integrity are not going to permit the great mass of scientists to rely on the kind of obfuscation and misdirection that you have to keep that dying theory alive.

Although the battle between theologians and scientists regarding the origins of man and nature, has raged for decades, an accumulating amount of evidence seems to be causing some scientists to re-examine the role an intelligent designer might have played in the origins of life.

[dr_lew]

Well, this is all a quibble on the meaning of "complex" I suppose, but do you really believe you can hold hydrogen in your mind? - like a poker hand or something?

[Pan_Yan]

Ah Yes... as with all these threads the "My side must be right because I can post a longer thesis as a reply than you can" theory has kicked in.

Don't get made, one of the creationists will post a reply in a minute, so it's not a partisan argument.

[DouglasKC]

Although the battle between theologians and scientists regarding the origins of man and nature, has raged for decades, an accumulating amount of evidence seems to be causing some scientists to re-examine the role an intelligent designer might have played in the origins of life.

That's a good point. If it were simply a matter of a few religious nuts making noise than these threads wouldn't exist. What scientist would debate the doctrine of baptism on scientific merit? The reason it's such a lively debate is exactly because it has merit within the scientific community.

[GSHastings]

Evolution does not even attempt to explain where something once came from nothing. It explains the progress- this turned to this which turned to that- but not where Life began.

That seems to be the primal cop-out of evolutionist these days. They like to pretend that evolutions doesn't try to explain the origins of life. When in fact it does, and they truly believe that it does. They think that the same process of chance events resulted in the formation of life.

As we speak, members of the evolution religion have their robots roaming around on Mars, pationately hoping to prove that Life occured on MARS.

The first living thing (which no one has even been able to define what that would be) would by definition have to be a SPECIES.

If Evolution cannot explain the occurance of the first species, then Darwin should have titled his book something like "Evolution: The Origins of Species (except one)".

[Fester Chugabrew]

If you asked me if I believe the Earth is round, that would be insulting.

Unless you've seen the earth from several hundred miles up I'd say you trust the pictures and testimony of other people. Maybe you've been up there already. I don't know. Buy why be insulted on account of a simple question? I believe the earth is round, and if anyone asked as much I'd answer the same, even though I have not seen it with my own eyeballs. I certainly would not count it an insult if someone asked. Good heavens, the earth is just the way God made it, and just the way He keeps it.

[Alamo-Girl]

Thanks for the ping!

[raygun]

One has to be careful with that argument, as computers aren't biological organisms. Neither are junkyards, so a tornado moving through one won't assemble a 747, and neither will a silicon and quartz based digitial watch assemble itself together. None of the components have a natural tendancy to organize and arrange themselves in that way.

You see, you'll be told you're guilty of making the strawman appeal to incredulity. Just because its mind-bogglingly complex or so improbable means it can't be that way by chance.

Biological organisms are much different though. Despite the greater the improbability of any arbitrary biological process, the fact that it actually exists means the possibility of it being is 100%. In fact with the natural order of things, the way they are is just the most likely way for them to be. The physical constants of the universe having to be each as precise as they are - both individually and in concert - each dependent upon all the others for their specific values, and the incomprehensible harmony of the mechanics of the universe is not collossally improbable, that's just the natural tendancy of the universe. Why argue about the seemingly improbable odds of left-handed proteins being required for all life, when identical but right-handed (chimeric) proteins would destroy the life being randomly assembled, the fact that it is that way shows that's the universes natural tendancy in being. Over the time of billions and billions of years, the natural tendancy would be for more left-handed proteins to assemble themselves, so obviously all biological process are going to be dependent on them. That's just pure logic. Why debate or argue about that? This is not a matter of faith or anything. It just is that way. Period. Creationists will tell you that God just is, so why can't evolutionists just have their is too?

Look, flipping a nickle 1000 times in a row and coming up heads is monumentally improbable, but if it happens then the possibility of that happening is 100%. Now for that to happen again would be even more remote of a probability, but if it does happen again, the possibility of it happening again would be 100%. Just because each of the components and physical constants of the universe in and of themselves have a higly improbable likelyhood of occuring, the fact they they all did simultaneously assemeble together into this universe means that the possibility of a universe constructed in the way it is is 100%.

[FireTrack]

"The six feet of DNA coiled inside every one of our body's one hundred trillion cells"

Tied end to end they would reach from the Earth to the Sun over 1200 times! Pretty amazing considering it is over 90 million miles to the Sun...

[dr_lew]

Speak for yourself. What kind of a role do you think an "intelligent designer might have played in the origins of life." Did he order others about? Did he mold clay with his "hands" ? Did he arrange molecules with tweezers, perhaps? Speak!

[Alamo-Girl]

Jeepers! Thanks for the illustration!

[raygun]

It doesn't matter. Doctors aren't biologists. And many biologists aren't even evolutionary biologists. And the opinion of anybody who's not an evolutionary biologist doesn't matter anyways. But evolution is absolutely true so it has to be taught to everbody, lest people shun science and begin believing in magic (or that the earth is flat).

Any doctor, who's also a Christian must (by definition) also be a Chrisitan evolutionist, or they're definitely not a doctor anybody would want to go to, because evolution is essential to the science of biology, which is esential to the study and practice of medicine. BUT it really doesn't matter one way or the other since doctors aren't biologists.

Ergo, you don't have a point.

[Ichneumon]

How about blood clotting? How can blood clotting develop over time, step by step, without bleeding to death in the meantime?

See below.

The whole system needs to be in place.

No it doesn't. There are animals that get along just fine with only a portion of the vertebrate clotting system. Nice try. Learn some science before you attempt to critique it.

Clot in lung, you die. Clot 30 minutes after a cut, you die. Clot throughout your whole body, you die. Clot that doesn't cover the whole cut, you die.

Modern vertebrates have come to critically depend upon the clotting system they've got now. However, when the current system was being evolved from simpler systems, the life forms which had those simpler systems didn't require anything as complex as our current system. A so-so clotting system is still better than none at all, especially for an organism that has other ways of dealing with vascular injury (or lower blood pressure compared to ours, or different blood composition which doesn't "leak out" as readily as ours, etc.) and doesn't put "all its eggs" in the one basket of blood clotting.

A huge amount of the evolutionary history of the modern blood clotting system has already been reconstructed, like which cascades were added in what lineages when, and based on what mutational changes -- most of what remains are just some of the finer details. Funny how the creationists sort of "forget" to mention that when they hand-wave about the "enormous complexity" of the blood clotting system, eh? Behe even goes so far as to falsely claim that nothing whatsoever is known on this subject -- he's either lying or is inexcusably incompetent, but neither option inspires confidence.

From a previous post of mine:

Now, also, you omitted all references to the blood clotting stuff.

...because Behe has already been hammered on that point thorougly enough that he has pretty much stopped using it as an "example". He has been concentrating on the flagellum mostly, thus the focus of my response.

For pete's sake, lets get comprehensive here! In detail, discuss why gradual evolution of blood clotting with 10 protein feedback loops all working at once is actually quite feasible evolutionarily speaking.

Well, okay, since you insist... Check out The Evolution of Vertebrate Blood Clotting, or The evolution of vertebrate blood coagulation as viewed from a comparison of puffer fish and sea squirt genomes. Excerpt from the latter paper:

It is thought that 50–100 million years separate the appearances of urochordates (which include the sea squirt) and vertebrates. During that time the machinery for thrombin-catalyzed fibrin formation had to be concocted by gene duplication and the shuffling about of key modular domains. The relative times of duplicative events can be estimated by various means, the most obvious being the presence or absence of a gene in earlier diverging organisms, although it must be kept in mind that lineages may lose genes. Another way to gauge events is from the relative positions of various gene products on phylogenetic trees, earlier branching implying earlier appearance. In this regard, (pro)thrombin invariably appears lower on the phylogenetic trees than do the other vitamin K-dependent factors (Fig. 2).

The order of events can also be inferred by considering the most parsimonious route to assembling the various clusters of peripheral domains. Nine of the proteases under discussion can be accounted for by six domain-swapping events (Fig. 5). Indeed, the presence of a multiple-kringle protease in the sea squirt genome provides a reasonable model for a step-by-step parallel evolution of the clotting and lysis systems. It should be noted that a serine protease with only one kringle has been found in the ascidian Herdmania momus (36). Although numerous scenarios have been offered in the past about how modular exchange was involved in generating these schemes (refs. 4, 12, and 37–41, inter alia), the new genomic data now provide a realistic set of starting materials.

Also, Evolution of enzyme cascades from embryonic development to blood coagulation:

Recent delineation of the serine protease cascade controlling dorsal-ventral patterning during Drosophila embryogenesis allows this cascade to be compared with those controlling clotting and complement in vertebrates and invertebrates. The identification of discrete markers of serine protease evolution has made it possible to reconstruct the probable chronology of enzyme evolution and to gain new insights into functional linkages among the cascades. Here, it is proposed that a single ancestral developmental/immunity cascade gave rise to the protostome and deuterostome developmental, clotting and complement cascades. Extensive similarities suggest that these cascades were built by adding enzymes from the bottom of the cascade up and from similar macromolecular building blocks.

That was the abstract. An excerpt from the text:

The downstream protease of the vertebrate clotting cascade (Fig. 1d), thrombin, belongs to the same lineage as complement factors C1r and C1s. The upstream and middle proteases of the clotting cascade (factors VII, IX and X) belong to the most modern lineage, that of horseshoe crab clotting factor C. Therefore, the lineage of thrombin is parental to that of the upstream and middle proteases of the clotting cascade (Table 1) and distinguishes it from the other vitamin-K-dependent clotting proteases (factors VII, IX and X, and protein C). This conclusion agrees with sequence and species comparisons implying that thrombin was the ancestral blood-clotting protein [11]. It also suggests that vertebrate blood clotting emerged as a by-product of innate immunity, because the entire functional core of vertebrate clotting shares ancestry with complement proteases.

And if that's not enough, you could check these out:

Banyai, L., Varadi, A. and Patthy, L. (1983). “Common evolutionary origin of the fibrin-binding structures of fibronectin and tissue-type plasminogen activator.” FEBS Letters, 163(1): 37-41.

Bazan, J. F. (1990). “Structural design and molecular evolution of a cytokine receptor superfamily.” Proceedings of the National Academy of Sciences of the United States of America, 87(18): 6934-6938.

Blake, C. C. F., Harlos, K. and Holland, S. K. (1987). “Exon and Domain Evolution in the Proenzymes of Blood Coagulation and Fibrinolysis.” Cold Spring Harbor Symposia on Quantitative Biology: The Evolution of Catalytic Function, LII: 925-932.

Fornace AJ Jr, Cummings DE, Comeau CM, Kant JA, Crabtree GR. “The Structure of the human gamma-fibrinogen gene. Alternate mRNA splicing near the 3' end of the gene produces gamma A and gamma B forms of gamma-fibrinogen.” J Biol Chem. 1984 Oct 25;259(20):12826-30.

Crabtree, G. R., Comeau, C. M., Fowlkes, D. M., Fornace, A. J., Jr., Malley, J. D. and Kant, J. A. (1985). “Evolution and structure of the fibrinogen genes: Random insertion of introns or selective loss?” Journal of Molecular Biology, 185(1): 1-20.  

Di Cera, E., Dang, Q. D. and Ayala, Y. M. (1997). “Molecular mechanisms of thrombin function.” Cell Mol Life Sci, 53(9): 701-730.  

Doolittle, R. F. (1985). “More homologies among the vertebrate plasma proteins.” Biosci Rep, 5(10-11): 877-884.

Doolittle, R. F. (1990). “The Structure and Evolution of Vertebrate Fibrinogen A Comparison of the Lamprey and Mammalian Proteins,” in ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY: FIBRINOGEN, THROMBOSIS, COAGULATION, AND FIBRINOLYSIS. C. Y. Liu and Chien, S. New York, Plenum Press. 281.

Doolittle, R. F. (1992). “A detailed consideration of a principal domain of vertebrate fibrinogen and its relatives.” Protein Science, 1(12): 1563-1577.

Doolittle, R. F. (1992). “Early Evolution of the Vertebrate Fibrinogen Molecule.” Biophysical Journal, 61(2 PART 2): A410.  

Doolittle, R. F. (1992). “Stein and Moore Award address. Reconstructing history with amino acid sequences.” Protein Science, 1(2): 191-200.

Doolittle, R. F. (1993). “The Evolution of Vertebrate Blood Coagulation - a Case of Yin and Yang.” Thrombosis and Haemostasis, V70(N1): 24-28.

Doolittle, R. F. and Feng, D. F. (1987). “Reconstructing the Evolution of Vertebrate Blood Coagulation from a Consideration of the Amino Acid Sequences of Clotting Proteins.” Cold Spring Harbor Symposia on Quantitative Biology: The Evolution of Catalytic Function, LII: 869-874.

Doolittle, R. F., G., Spraggon and J., Everse S. (1997). “Evolution of vertebrate fibrin formation and the process of its dissolution.” Ciba Found Symp, 212: 4-17; discussion 17-23.

Doolittle, R. F. and Riley, M. (1990). “The amino-terminal sequence of lobster fibrinogen reveals common ancestry with vitellogenins.” Biochemical and Biophysical Research Communications, 167(1): 16-19.

Edgington, T. S., Curtiss, L. K. and Plow, E. F. (1985). “A linkage between the hemostatic and immune systems embodied in the fibrinolytic release of lymphocyte suppressive peptides.” Journal of Immunology, 134(1): 471-477.  

Ghidalia, W., Vendrely, R., Montmory, C., Coirault, Y., Samama, M., Lucet, B., Bellay, A. M. and Vergoz, D. (1989). “Overall study of the in vitro plasma clotting system in an invertebrate, Liocarcinus puber (Crustacea Decapoda): Considerations on the structure of the Crustacea plasma fibrinogen in relation to evolution.” Journal of Invertebrate Pathology, 53(2): 197-205.  

Hervio, L. S., Coombs, G. S., Bergstrom, R. C., Trivedi, K., Corey, D. R. and Madison, E. L. (2000). “Negative selectivity and the evolution of protease cascades: the specificity of plasmin for peptide and protein substrates.” Chemistry & Biology, V7(N6): 443-452.  

Hewett-Emmett, D., Czelusniak, J. and Goodman, M. (1981). “The evolutionary relationship of the enzymes involved in blood coagulation and hemostasis.” Annals of the New York Academy of Sciences, 370(20): 511-527.  

Holland, S. K., Harlos, K. and Blake, C. C. F. (1987). “Deriving the generic structure of the fibronectin type II domain from the prothrombin Kringle 1 crystal structure.” EMBO (European Molecular Biology Organization) Journal, 6(7): 1875-1880.  

Jordan, R. E. (1983). “Antithrombin in vertebrate species: conservation of the heparin-dependent anticoagulant mechanism.” Archives of Biochemistry and Biophysics, 227(2): 587-595.  

Kant, J. A., Fornace, A. J., Jr., Saxe, D., Simon, M. J., McBride, O. W. and Crabtree, G. R. (1985). “Evolution and organization of the fibrinogen locus on chromosome 4: Gene duplication accompanied by transposition and inversion.” Proceedings of the National Academy of Sciences of the United States of America, 82(8): 2344-2348.  

Kornblihtt, A. R., Pesce, C. G., Alonso, C. R., Cramer, P., Srebrow, A., Werbajh, S. and Muro, A. F. (1996). “The fibronectin gene as a model for splicing and transcription studies.” FASEB Journal, 10(2): 248-257.  

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Pan, Y. and Doolittle, R. F. (1992). “cDNA sequence of a second fibrinogen alpha chain in lamprey: an archetypal version alignable with full-length beta and gamma chains.” Proceedings of the National Academy of Sciences of the United States of America, 89(6): 2066-2070.

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Patthy, L. (1990). “Evolution of blood coagulation and fibrinolysis.” Blood Coagulation and Fibrinolysis, 1(2): 153-166.

Patthy, L. (1990). “Evolutionary Assembly of Blood Coagulation Proteins.” Seminars in Thrombosis and Hemostasis, 16(3): 245-259.

Patthy, L. (1999). “Genome evolution and the evolution of exon-shuffling—a review.” Gene, 238(1): 103-114.

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Wang, Y. Z., Patterson, J., Gray, J. E., Yu, C., Cottrell, B. A., Shimizu, A., Graham, D., Riley, M. and Doolittle, R. F. (1989). “Complete sequence of the lamprey fibrinogen .alpha. chain.” Biochemistry, 28(25): 9801-9806.  

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The 2.0-Å crystal structure of tachylectin 5A provides evidence for the common origin of the innate immunity and the blood coagulation systems

Davidson CJ, Tuddenham EG, McVey JH. 450 million years of hemostasis J Thromb Haemost. 2003 Jul;1(7):1487-94.

And so on...