Wheat-dogg's World

Molecular Biology: The Origin of Life

This section of the Leader’s Guide confuses, deliberately or otherwise, evolution with abiogenesis. Evolution deals with the development of organisms in response to their environment. Abiogenesis is a separate theory that suggests that conditions on the early Earth were favorable to bring organic molecules to develop into the first living organisms.

Guide:
“Darwinian evolution argues that life arose from a primordial sea on a lifeless planet through a chance collision of chemicals, and that over billions of years, this biological accident gave rise to all of life, including humans. In other words: NOTHING + TIME AND CHANCE = EVERYTHING. Modern science has now revealed incredible problems with this explanation.”

Comments:
The age of the Earth is reliably estimated at 4.6 billion years. The accretion of matter from the early solar system resulted in a young Earth that was very hot, very dry and devoid of oxygen. Volcanism brought water in the form of steam from underground. As the Earth cooled from its formation, water condensed and formed the first oceans. The theory of abiogenesis proposes that the chemicals dissolved in surface water, or in tidal pools, developed through processes not fully understood into the first living organisms within the first billion years of Earth’s existence.

Now, the Guide’s “equation of life” is catchy, but not true. In fact, there was something. Astronomers have detected simple organic molecules, methane, ethane, formaldehyde, where there is no evidence of life throughout the universe. The building blocks of proteins, carbohydrates and other biochemicals are not limited to present-day Earth. A billion years is an awfully long time, and these ingredients were all over Earth, so abiogenesis is not as far-fetched as it sounds. We just do not know precisely how biochemistry developed out of abiochemistry. Science does not take a shortcut and say some intelligence played around with this global chemistry set.

Guide:
We now come to a discussion of the living cell, in which the writers argue that Darwin and his contemporaries knew little of the complex biochemistry of the cell. The nucleus of the cell contains an enormous amount of information, “as much digital information in its DNA as the Encyclopedia Britannica — ”all thirty volumes — three or four times over.”

And where does this information come from?

“Dr. Stephen Meyer points out that
‘Everything we know from our uniform and repeated experience is that information always comes from an intelligent source. So when we find information in the cell in the form of the digital code in DNA, the most likely explanation is that DNA also had an intelligent source.’”

Comment:
ID proponents repeatedly marvel over the digital information in DNA, and argue that information has to derive from intelligence to support their claim that a Designer made DNA. But they cannot offer any direct evidence that such an intelligence exists.

DNA does contain a lot of information, which is reproduced with surprisingly accuracy generation after generation. In a sense, DNA acts like a digital storage facility, comprising sequences of a 4-bit code (A C G T). The bacterium E. coli’s genome comprises 4.6 million pairings of A C G and T, while the human genome has about 3 billion pairs. Comparing E. coli’s memory to that of a computer processor, one group of researchers estimated E. coli’s DNA has a capacity of about 1 Megabyte. Using that as a benchmark, we could say the human genome’s capacity is about 700 Megabytes.

That’s a lot, but not appreciably more than that of the Encyclopedia Britannica. The EB occupies between 100 Megabytes to 1 Gigabyte (1024 Megabytes) of digital data, depending on which source you use. To say a cell’s DNA could hold three or four EB’s worth of data is grossly inaccurate, yet this factoid is mindlessly repeated all over creationist/ID sites.

And if DNA does contain a lot of data (much of which is junk DNA, meaning it serves no useful purpose in replication), so what? If we assume that DNA molecules have existed for the last 3 billion years, what is so surprising about the amount of information they carry?

Stephen Meyer is one of the co-founders of the Discovery Institute, an ID thinktank in Seattle. The quote here repeats a version of the old “watchmaker” hypothesis: if we find a complex object on the ground, say a pocket watch, we immediately would assume it was the product of an intelligent designer. ID scholars frequently claim that information can only come from intelligent sources, ignoring general information theory that assumes information can come from anywhere. For example, from core samples of the ocean floor, we know that the magnetic field of the Earth has flip-flopped many times over millions of years. That’s information, and it did not derive from an intelligence but from natural causes. Likewise, the information encoded in DNA results from billions of years of evolution, not a Designer.

Guide:
Continuing the massive information theme, we read:

Modern high-speed supercomputers have now used large-scale number crunching to calculate the eons of time and probabilities that are required to develop a cell through chance and mutation. The result? The odds are essentially zero, no matter how many millions or billions of years pass.

The famous astronomer Sir Fredrick Hoyle (Professor, and Founder of the Institute of Astronomy, Cambridge University) compares the probability of spontaneous life to lining up 1×10⁵⁰ (one with 50 zeros after it) blind people, giving them each a scrambled Rubik’s cube, and finding that they all solve the cube at the same moment.

Comment:
Notice we have no citations of who performed such calculations, or when they were done, just a flat assertion that they were done and had resulted in a null answer. ID proponents like to offer these perhaps fictional computer simulations as proof that abiogenesis could never have happened, but fail to recognize that simulations — even with supercomputers — are just that, models of what might have happened. Simulations are not evidence.

Have supercomputers modeled cell development “from scratch?” I could not find any independent references of such a project. Supercomputers have been used to simulate yeast cell division, taking 20,000 CPU hours on a 2200-processor parallel computer. They have replicated a virus and the ribosome .

Hoyle is an important pioneer in astrophysics who rejected both the Big Bang theory and abiogenesis. Critics of his Rubik’s cube manipulation metaphor call it “Hoyle’s fallacy,” saying he assumed incorrectly that early organisms had to be as complex as modern one and that he ignored the “parallel processing” going on throughout the early Earth and the amount of time available for such genetic trial and error. It’s an intriguing thought experiment, but a poor model of abiogenesis.

Guide:
Yet another pullout quote:

There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system, only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation for such a vast subject –evolution — with so little rigorous examination of how well its basic theses work in illuminating specific instances of biological adaptation or diversity.

- Dr. James Shapiro (Professor of Microbiology, University of Chicago)

And another, from a well-known ID-friendly biochemist:

Dr. Michael Behe (Professor of Biochemistry, Lehigh University) says, “Molecular evolution is not based on scientific authority. There is no publication in the scientific literature — in prestigious journals, specialty journals, or books — that describes how molecular evolution of any real, complex, biochemical system either did occur or even might have occurred.”

Comments:
Again the guide confuses evolution with other biological theories, and tries to paint a picture of “Darwinism” as fatally flawed because it cannot explain absolutely everything biological. The development of biochemistry is not part of the theory of evolution, but rather an extension of abiogenesis. Evolution deals with organisms and populations, not with molecular biology.

Shapiro is a geneticist at the University of Chicago. While critical of evolution, he is by no means a proponent of ID. The quote ironically comes from his largely negative review of Behe’s book, Darwin’s Black Box: The Biochemical Challenge to Evolution. Shapiro recognizes that evolutionary theory does not have all the answers, but unlike Behe and other ID proponents is not willing to throw the baby out with the bathwater. See this debate here between Shapiro and some IDists.

Behe is more willing to toss out evolutionary theory, having written tomes suggesting Intelligent Design is the only explanation for complex biological structures. He has been called as an expert witness in court challenges to evolution instruction in schools; his testimony defending ID as a viable alternative has generally been highly ineffective.

Guide:
The Expelled propagandists now attack the science of genetics, a necessary corollary to the theory of evolution, by bringing up dog breeding as evidence against evolution.

Those classic textbooks depicting various breeds of dogs as “evolution in action”  are misleading. Why? Because all those poodles, labs, and shepherds are still dogs! Yes, there is evidence of change within a species, but there is no evidence of one species changing into a truly different form. Breeding essentially mixes and matches among all the genes in an existing gene pool, much like you would shuffle and deal a deck of cards. But breeding cannot create new genes, any more than shuffling a deck can create new cards. Plus, selective breeding of plants and animals is a process guided by intelligence, not mere chance and survival of the fittest — unlike Darwinian evolution.

Comments:
Darwin himself referred to pigeon breeding in The Origin of Species as a means to demonstrate how selection can affect future generations of pigeons. He never suggested that natural selection was identical to selective breeding, however. Breeding is artificial selection for specific traits. Natural selection “breeds” for resilience, adaptability and survival. Dog breeders and pigeon breeders do not want offspring of their animals to die, and they do not have the luxury of millions of years to force a new species from dogs or pigeons. Further the environmental pressures on domesticated dogs and pigeons are nil.

Besides, having reviewed quite a few high school science textbooks over the last 25 years, I can safely say the majority of them are plain awful, with many errors and misconceptions

Guide:
On to mutations, which the Guide summarily dismisses as unlikely to have created complex organisms.

Scientists are still struggling to understand the full impact of mutations on living things, but what they do know is that the vast majority of mutations are damaging to an organism or neutral. Far less than one percent might actually be beneficial. So how can incomprehensibly complex organisms be the result of mutations that are rarely if ever beneficial?

As biologist Lynn Margulis at the University of Massachusetts, Amherst, has concluded:
“New mutations don’t create new species; they create offspring that are impaired.”

Comments:
This dismissal of the role of mutations is naive, and (surprise) misleading. While it is true that most mutations (from interactions with radioactivity, cosmic rays or glitches in DNA replication) are not beneficial, the rare few that are beneficial survive into future generations. With billions of years and a vast population available to evolution, there was ample opportunity for mutations to successfully change past organisms permanently. We may be the result of such mutations. We cannot know the fate of unsuccessful ones.

Tracking down the source of this quote by Margulis took some work. It pops up repeatedly on anti-evolution sites without so much as a citation on most. It comes from an interview she gave the Brattleboro (Vt.) Reformer before her participation in a debate about evolutionary theory. It is not from her own work or research, so the accuracy of the quote, its meaning and importance are somewhat cloudy. Margulis is, like Shapiro, a critic of both evolutionary theory and ID, so her statement should not be construed as favoring ID at all.

Here is the quote in context:

Neo-Darwinism includes a theory of random mutation of genes.

“Random mutation indisputably exists,” said Margulis in an interview Thursday. “But I claim that new mutations don’t create new species; they create offspring that are impaired.”

“Intelligent design says that random mutation could not account for the sophisticated life around us. It had to have a designer,” said Margulis. “Well, between 1850 and 1950, in what we now think of as southern California, skyscrapers and highways and a movie industry rose out of nothing and it all fits together — well, sort of. And they’d say, ‘Oh my God — it had to be designed, it just came out of nowhere.’ But that doesn’t take any history into account, like the geographic background of southern California or the origin of electricity.”

“I wouldn’t suppress [intelligent design proponents'] argument. But you have to be aware of the agenda,” she said.

Notice once again that the Guide is still arguing against evolution (and abiogenesis), not by providing evidence supporting ID, but by arguing against evolution. There’s not one shred of “scientific research” disproving evolution or abiogenesis, just appeals to reject the oversimplified characterizations of the theories as absurd. It’s a classic straw-man argument, and logically invalid.

Onward!

Guide:
Continuing with its discussion of molecular biology, the Guide presents “irreducible complexity,” another cornerstone of ID.

A system is considered irreducibly complex if it consists of several interrelated parts so that removing even one part destroys the system’s function. Much if not most of the biological machinery present in the cell exhibit such irreducibly complex structures.

The Guide then goes on to use a mousetrap and the bat as counterexamples of evolution.
In order for a mousetrap (a model for a successful organism) to work, all of its parts must be present at once. If any part were not present, the mousetrap could not catch mice and thus, die out.

“Evolutionists” — notice the pejorative term — “believe the bat evolved from a mouse-like creature whose forelimbs gradually evolved into wings. But think through this evolutionary progression: The mouse’s front limbs mutate and grow longer, and skin begins to grow between the toes. Now the animal can’t run without stumbling, yet its forelimbs are not long enough to function as wings. So during this transitional stage, the mouse-bat has limbs too long for running and too short for flying. Unable to efficiently get around, it would become extinct.”

Comments:
Irreducible complexity is the brainchild of Michael Behe, a biochemist at Lehigh University quoted earlier in the Guide. Behe rejects the gradualism inherent in evolution as an unlikely explanation for complex structures in organisms. The mousetrap model is his. Behe contends that an evolving organism could not survive if any one of the structures in it were not present. A compelling argument, if one requires a Designer be present to fashion the structures as Behe does. Something made the mousetrap whole, he says.

The bat example is an extension of the mousetrap model using a real animal. The argument is flawed, however, since it assumes a single creature and/or its immediate offspring had to develop from mouse to bat gradually, as described. In fact, evolution involves entire populations of mice, not a single family. Rodents are prolific little critters. One could (if willing) accept the possibility that mouse A with long webbed toes met mouse B with long forelegs to produce mice C through Z with various combinations of both features. Unsuccessful offspring woild die off, leaving ones with more useful body parts. Given enough time and many, many generations of rodents, a new kind of rodent could occupy an environmental niche in the trees in which long toes and forelegs were not a hindrance to survival. After more generations, wings would develop as toes, forelegs and webbing increase in size.

That modern mice and bats are related is very clear. Their basic morphology and metabolisms are similar, and they share many of the same genes.

Besides, this argument sounds awfully like creationism, which proposes that all organisms were created whole as we see them now. IDists try to argue (unconvincingly and largely unsuccessfully, see Kitzmiller v. Dover) that ID is not creationism. This section offers no alternative explanation or mechanism for the mouse-bat connection. It just reduces evolutionary arguments to oversimplified conundrums.

Guide:
As a segue to paleontology, we read this:

It is difficult to explain or imagine how bat wings could have been formed in unplanned gradual stages — which may be why there is no geological evidence of this “transitional” process; the first time bats appear in the fossil record, they are fully formed, with wings.

Comments:
ID proponents (and creationists, too) raise the canard of missing “transitional fossils” repeatedly, contending that if transitional organisms existed, their remains must have been fossilized at one time or another. In so doing, they choose to ignore the equally valid evidence that the fossil record is spotty. Fossilization happens only under certain rare geological conditions, so the vast majority of organisms never become fossils. There are “transitional fossils” for some organisms, enough in fact to support evolution’s hypothesis that one species can gradually give rise to another. We just don’t have every single one.

Guide:
More Darwin quotes:

If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.

To suppose that the eye, with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest degree.

Comments:
Well, first of all, finding evidence contradicting any theory is the surest way to bring a theory down. Science never proves a theory correct, but it can disprove it. That Darwin recognized the reliance of his theory on supporting evidence just means he was a good scientist. Besides, the quote leaves off Darwin’s closing sentence, “But I can find out no such case.”

The second quote is incomplete, a typical behavior of ID proponents when they want to turn Darwin’s words apparently against him. It comes from Chapter 6 of The Origin of Species:

To suppose that the eye with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest degree. Yet reason tells me, that if numerous gradations from a perfect and complex eye to one very imperfect and simple, each grade being useful to its possessor, can be shown to exist; if further, the eye does vary ever so slightly, and the variations be inherited, which is certainly the case; and if any variation or modification in the organ be ever useful to an animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, can hardly be considered real. How a nerve comes to be sensitive to light, hardly concerns us more than how life itself first originated; but I may remark that several facts make me suspect that any sensitive nerve may be rendered sensitive to light, and likewise to those coarser vibrations of the air which produce sound.

In fact, there are organisms still with very primitive “eyes” — areas that are sensitive to light — that look nothing like the mammalian eye.

The writers of the Expelled Guide have quote-mined famous scientists, choosing quotes that appear to support their thesis, offered thought experiments and simulations as evidence, and when making connections between “evidence” and conclusion, wave their hands around and say, “a designer did it.” There’s still no identifiable “new scientific research” as proposed in the Introduction.

Furthermore, the Guide does nothing more than rehash material present on dozens of ID websites, which incestuously use each other’s content without regard for checking original sources or citing those sources. If ID is such a new and vibrant theory, why doesn’t it have something new to say?

Next up: Paleontology