Theory of Intelligent Design, the best explanation of Origins

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Evolutionary leftovers are common

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1 Evolutionary leftovers are common on Wed Jul 16, 2014 6:35 pm


Evolutionary leftovers are common


Biological designs have always fascinated thinkers even if those designs were not well understood. Even as late as the nineteenth century, when Darwin developed his theory of evolution, there was substantial ignorance of how biology worked. Before Darwin, William Paley had written of a “secret spring” to describe the complex designs he believed must exist within organisms. A complicated watch, like biological organisms, used energy to function. But watches did not obtain their own energy in the first place, or make new watches, as did biological organisms. [1] Organisms, reasoned Paley, must indeed have unseen complexities.

But Paley worked within the design perspective. With Darwin’s theory of evolution, that perspective dramatically shifted. Darwin speculated that life first might have arisen in a warm little pond where protein molecules happened to assemble to form the first living entity. [2] If organisms arose via such unguided, natural processes then one should hardly expect elegant designs or clever mechanisms. The fundamental unit of life, the cell, was typically characterized as a mere building block or as an elementary organism, rather than complex machine, [3] and evolutionists interpreted the biological world to be full of clumsy designs. [4]


As evolutionary thinking took hold, organisms were increasingly viewed as clumsy and happenstance contraptions. In 1871 Darwin’s book The Descent of Man listed several structures in the human body he thought had become unimportant in the evolutionary process. Darwin argued that via the evolutionary process the appendix, for instance, had reduced in length and was now useless. This was the evolutionary expectation.

In 1888 the American evolutionist Joseph Le Conte added to this list of evolutionary leftovers he argued existed in various animals. The whale’s teeth and the embryonic development of fish, revealed the crude works of evolution.

In 1893 German anatomist Robert Wiedersheim added to Darwin’s list and found eighty-six organs he deemed to be evolutionary leftovers and of less physiological significance than they once were. Adenoids and tonsils, lymphatic tissues, the pineal, pituitary, thyroid and thymus glands, ear muscles, body hair and the three smallest toes all made Wiedersheim’s list of structures that were supposed to be losing their importance as the human body evolved. In later years Wiedersheim’s list grew and even was invoked in the famous Scopes Monkey Trial to argue that humans are “a veritable walking museum of antiquities.”

Darwin’s expectation that evolution would leave a trail of decaying structures continued in the twentieth century. As evolution was envisioned to produce new species and new designs, it was thought the path inevitably would be littered with leftover designs because life was assumed to be the product of unintelligent forces of nature.

All of this means that when new designs were first investigated they often were assumed to be rather simple. If the workings of new biological findings were confusing or not understood, then evolutionists typically would assume a minor function, if any at all. These expectations have consistently been wrong.


The parts of the human body that evolutionists thought to be evolutionary relics have mostly turned out to be important and even contrary to the expected evolutionary trend. The importance of our toes, tonsils and most of Wiedersheim’s other eighty-four parts is now better understood, and comparative anatomy has not fulfilled the evolutionary expectation of decaying structures.

For instance, the pineal gland is now known to be part of the endocrine system that sends chemical messages (hormones) in the blood and interacts with the nervous system. Wiedersheim also claimed the coccyx, a short collection of vertebrate at the end of the spine, was an evolutionary leftover. But the coccyx is the attachment point for several important muscles and ligaments. The thyroid gland consists of two lobes on either side of the wind pipe and produces thyroxine which regulates cellular metabolism. It is important in cold temperatures and in child growth. The thyroid gland also produces calcitonin which helps regulate blood calcium levels. Its malfunction and enlargement—the disease known as goiter—is visible as a swelling of the front of the neck. Both the thymus gland and the appendix contribute to the body’s immune system. Our appendix was thought to be a shriveled-up remnant because it was shorter than that of the rabbit’s. But the appendix has since been found to be larger and more distinct than its counterpart in the other primates. [5]

Perhaps more important are the many findings of subtle and sophisticated designs in biology that consistently defy the evolutionist’s expectations. Consider, for example, the process of cell division which requires an exacting sequence of elaborate and complex steps to be followed, controlled by an array of biochemicals. [6] And after the contents of the cell have been duplicated, the cell quickly constructs a short-lived ring structure that contracts and splits the cell into the two daughter cells. [7]

Imagine an automobile duplicating all of its parts, and then splitting itself in two. One review summarized cell division as a remarkable process “during which cells undergo profound changes in their structure and physiology. These events are orchestrated with a precision that is worthy of a classical symphony, with different activities being switched on and off at precise times and locations throughout the cell.” [8]

As Bruce Alberts, an evolutionist and President of the National Academy of Sciences, once wrote, “

We have always underestimated cells. Undoubtedly we still do today. But at least we are no longer as naive as we were when I was a graduate student in the 1960s. Then, most of us viewed cells as containing a giant set of second-order reactions: molecules A and B were thought to diffuse freely, randomly colliding with each other to produce molecule AB—and likewise for the many other molecules that interact with each other inside a cell. This seemed reasonable because, as we had learned from studying physical chemistry, motions at the scale of molecules are incredibly rapid. … But, as it turns out, we can walk and we can talk because the chemistry that makes life possible is much more elaborate and sophisticated than anything we students had ever considered. Proteins make up most of the dry mass of a cell. But instead of a cell dominated by randomly colliding individual protein molecules, we now know that nearly every major process in a cell is carried out by assemblies of 10 or more protein molecules. And, as it carries out its biological functions, each of these protein assemblies interacts with several other large complexes of proteins. Indeed, the entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines. […]

Why do we call the large protein assemblies that underlie cell function protein machines? Precisely because, like the machines invented by humans to deal efficiently with the macroscopic world, these protein assemblies contain highly coordinated moving parts. Within each protein assembly, intermolecular collisions are not only restricted to a small set of possibilities, but reaction C depends on reaction B, which in turn depends on reaction A—just as it would in a machine of our common experience. […]

We have also come to realize that protein assemblies can be enormously complex. … As the example of the spliceosome should make clear, the cartoons thus far used to depict protein machines (e.g., Figure 1) vastly underestimate the sophistication of many of these remarkable devices. [9]

Darwin’s theory predicts that we should find the leftovers of the evolutionary process, not sophisticated machines. But despite his ruminations of how these evolutionary expectations were unmet, Alberts continued to use evolution as his guide later in the article. And years later evolutionists continued to be astounded. As one researcher exclaimed a decade later, “It’s amazing to us. We thought the cell was so simple.” [10]

Evolution is not an intelligent process so evolutionists are amazed by what we find in biology. There is another reason why evolution expected cells to be relatively simple, and it stems from a fundamental tenet of evolutionary theory. A key premise of the theory is that genetic mutations are the main fuel for evolutionary change. That is, it has been a fundamental tenet of evolution that DNA gene mutations are an important source of the unguided biological variation upon which natural selection acts to morph one species into the next. Thus evolutionists focused narrowly on the genes in the DNA molecule. As one science writer put it, genes were at the center of the biological universe, much as ancient astronomers believed sun and stars revolved around the earth. [11]

Evolutionists compared genes across the different species to understand better their evolutionary relationships. For according to evolution, changes in those genes were the main cause of the origin of species. An obvious problem with this view arose when the human and chimp genes were found to be practically identical, with only minor differences between them. These differences could hardly explain the differences between the human and chimp, yet evolutionists ignored these obvious indications that genes play a less important role in determining the organism’s design. Indeed, evolutionists maintained the centrality of genes, and erroneously argued that the high genetic similarity between the human and chimp was powerful evidence for their common ancestry.

Now we know this picture to be substantially misguided. First, genes are far more varied and sophisticated than evolutionists expected. They can be edited in different ways and they even overlap on the same segment of DNA, like a sentence with a different message when read backwards.

And genes are only one part of a far more involved and complex story. Evolutionists were surprised when it was first discovered that genes comprise only a few percent of the DNA in higher organisms. If genes were so important, why did they comprise a tiny fraction of the genome? What was the role of all the non-genic DNA?

Such a large quantity of DNA must, it seemed, have a function. Yet some non-genic DNA varied substantially between even highly similar species. Evolution predicts that important DNA is preserved. It should be similar in similar species. In other words, similar species should not have DNA segments that are both substantially different and important.

The findings did not match evolutionary expectations and evolutionists could only guess at the role of all the non-genic DNA. A variety of minor functions were considered as well as the possibility that the majority of the genome was useless. Terms such as “junk,” “parasitic,” “selfish,” and “greedy” DNA were coined. [12] The genome increasingly was viewed as a motley collection of DNA, and this view fueled a new powerful argument for evolution, for only evolution would create such chaos.

Again the evolutionary expectations were substantially misleading. Not only have major, fundamental roles been discovered for much of the non-genic DNA, but its various functions are highly complex, far beyond anything evolutionists expected. One phenomenally complex example is the fine-tuned micro RNAs (MiRNAs) that perform a variety of regulatory jobs. [13]

Evolution did not expect this unseen complexity buried within the cell. As one evolutionist lamented, “The picture that’s emerging is so immensely more complicated than anyone imagined, it’s almost depressing,” [11]


The reaction of evolutionists to the important functionality discovered in what were believed to be evolutionary leftovers, and to the profound complexity found in biology, has been to ascribe the new found functionality and designs to evolution. All findings are consistently ascribed to the workings of evolution. The new functions and high complexity, say evolutionists, answer questions about how evolution works, not whether evolution works. Indeed, evolutionists are adept at integrating revolutionary findings into the evolutionary narrative. In new studies the once hapless non-coding DNA is now found to be a crucial player in the evolutionary process itself. [14,15,16] “It’s funny,” observed one evolutionist, “how quickly the field is now evolving.” [15]

Second, all of these failed expectations have not deterred evolutionists from their view of biology as a hodge-podge. Where function is still uncertain, the evolution literature is rife with explanations of evolutionary leftovers and haphazard designs. This is not surprising as this expectation is fundamental to the theory.


1.    Cornelius Hunter, Science’s Blind Spot: The Unseen Religion of Scientific Naturalism (Grand Rapids: Brazos, 2007), 108.
2.    C. Darwin The Life and Letters of Charles Darwin, ed. Francis Darwin (London: John Murray 1887, Vol. III), 18.
3.    Andrew Reynolds, “The cell’s journey: From metaphorical to literal factory,” Endeavour 31 (2007): 65-70.
4.    Cornelius Hunter, Darwin’s God: Evolution and the Problem of Evil (Grand Rapids: Brazos, 2001), 85-96.
5.    Laura Spinney, “The old curiosity shop,” NewScientist 17 May 2008, 42-5.
6.    M. Sullivan, D. O. Morgan, “Finishing mitosis, one step at a time,” Nature Reviews: Molecular Cell Biology 8 (2007): 894-903.
7.    “How Molecular Muscles Help Cells Divide,” Science Express, December 13, 2007.
8.    S. Ruchaud, M. Carmena, W. C. Earnshaw, “Chromosomal passengers: conducting cell division,” Nature Reviews: Molecular Cell Biology, 8 (2007): 798-812.
9.    Bruce Alberts, “The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists,” Cell 92 (1998): 291-294.
10.  University of California – San Diego, “Cellular message movement captured on video." ScienceDaily 3 June 2007.
11.  C. Nickerson,  “DNA unraveled,” Boston Globe  September 24, 2007.
12.  M. Morgante, “Plant genome organisation and diversity: the year of the junk!,” Current Opinion in Biotechnology 17 (2006): 168-173.
13.  G. T. Bommer, et. al., “p53-mediated activation of miRNA34 candidate tumor-suppressor genes,” Current Biology 17 (2007): 1298-1307.
14.  University of Bristol, “ ‘Junk DNA’ can explain origin and complexity of vertebrates, study suggests,” ScienceDaily 13 February 2008.
15.  Stanford University Medical Center, “ ‘Junk’ DNA now looks like powerful regulator, scientists find,” ScienceDaily 24 April 2007.
16.  S. B. Carroll, N. Gompel, B.Prudhomme, “Regulating evolution: How gene switches make life,” Scientific American, May, 2008.

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