Preaching bad design: An argument from ignorance?

Over the years many people have come with arguments that systems in nature are sub-optimal, or sub-par. These arguments were used as a means to point out that they are "dumb" designs if it was the product of mind.

An example of such an argument is given by Richard Dawkins. Take his article:
The Information Challenge

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Genomes are littered with nonfunctional pseudogenes, faulty duplicates of functional genes that do nothing, while their functional cousins (the word doesn't even need scare quotes) get on with their business in a different part of the same genome. And there's lots more DNA that doesn't even deserve the name pseudogene. It, too, is derived by duplication, but not duplication of functional genes. It consists of multiple copies of junk, "tandem repeats", and other nonsense which may be useful for forensic detectives but which doesn't seem to be used in the body itself.

Luckily science moves forward and these arguments from ignorance get left behind and the proponents of these arguments fade into history as proponents of ignorance trying to sell meaningless metaphysics.

Junk DNA is a myth.
Examples abound of research finding fascinating functions for these previously thought non-functional parts of the genome (out of ignorance and bad metaphysics-- Dawkins: "And there's lots more DNA that doesn't even deserve the name pseudogene.").

Model unravels rules that govern how genes are switched on and off

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"Since the discovery of DNA's double helical structure more than a half century ago, scientists have focused much of their attention on understanding the 2 percent of the genome that is made up of classic genes, which code for the production of proteins. However, the instructions for turning these genes on or off are generally not in the genes themselves. Rather, they are buried in the 98 percent of the genome that was once cast aside as little more than genetic "junk."

Scientists at CSHL uncover new RNA processing mechanism and a class of previously unknown small RNAs

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A very small fraction of our genetic material--about 2%-- performs the crucial task scientists once thought was the sole purpose of the genome: to serve as a blueprint for the production of proteins, the molecules that make cells work and sustain life. This 2% of human DNA is converted into intermediary molecules called RNAs, which in turn carry instructions within cells for protein manufacture. "And what of the other 98% of the genome? It has been assumed by many to be genetic junk, a massive accumulation of “code” that evolution has rendered superfluous. Now, however, scientists are discovering that the vast bulk of the DNA in our genomes, while it does not “code” for the specific RNA molecules that serve as templates for protein synthesis, do nevertheless perform various kinds of work."

'Junk' DNA May Have Important Role In Gene Regulation

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ScienceDaily (Oct. 20, 2008) — For about 15 years, scientists have known that certain "junk" DNA -- repetitive DNA segments previously thought to have no function -- could evolve into exons, which are the building blocks for protein-coding genes in higher organisms like animals and plants. Now, a University of Iowa study has found evidence that a significant number of exons created from junk DNA seem to play a role in gene regulation.

Well, it is not only supposedly "junk DNA" that was used for these kind of arguments. The vertebrate eye has been preached to be a bad design. Why? Why is it a bad design?

The human eye contain bona fide optical fibers to conduct light and here is a nice illustration. Besides the design arose 40-60 times during evolution, like evolution was biased (converged on an optimal design) towards such a structure. So why is it sub optimal? Are proponents of these arguments going to suggest a better design with all the blueprints? Thought not, arguments from ignorance are short on design.

Why was it suggested that the appendix is useless and functionless, instead of just admitting "we are still looking into it".
A few articles discussing its function:
1) Dasso JF. Howell MD. 1997. "Neonatal appendectomy impairs mucosal immunity in rabbits." Cellular Immunology. 182(1):29-37.
2) Dasso JF. Obiakor H. Bach H. Anderson AO. Mage RG. 2000. "A morphological and immunohistological study of the human and rabbit appendix for comparison with the avian bursa." Developmental & Comparative Immunology. 24:8:797-814.
3) Fisher, RE. 2000. "The primate appendix: a reassessment." The Anatomical Record (New Anatomist) 261:228-236.
4) Weinstein PD. Mage RG. Anderson AO. 1994. "The appendix functions as a mammalian bursal equivalent in the developing rabbit." Advances in Experimental Medicine & Biology. 355:249-53.
5) A more detailed survey of the evidence, with numerous references to other technical literature, showing that the appendix is not a vestigial organ can be found in J.W. Glover, The Human Vermiform Appendix—a General Surgeon’s Reflections, CEN Technical Journal, 3:31–38, 1988.

In short:
The appendix contains a high concentration of very specialized structures called lymphoid follicles (also found throughout the GIT). Lymphoid follicles in the appendix produce cells that produce antibodies that control which essential bacteria come to reside in the caecum and colon in neonatal life. The "strategic" placement of the appendix is important during the development of neonatal life in the setup of healthy intestinal flora therefore neonatal appendectomy will impair mucosal immunity.

"The appendix's job is to reboot the digestive system..." and "acts as a good safe house for bacteria,".

It might not be that important in later life and it can be removed, but so can your one kidney, your stomach, an eye, small intestines, reproductive organs etc. Are these bad designs then as well? See... these arguments have no force. Empty arguments from ignorance...



And the cilium? Until the 1990s, the prevailing view of the primary cilium was that it was merely a vestigial organelle, without important function (wiki). Seems like pretty high-tech structures to me?

Primary Cilium As Cellular 'GPS System' Crucial To Wound Repair

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ScienceDaily (Dec. 25, 2008) — The primary cilium, the solitary, antenna-like structure that studs the outer surfaces of virtually all human cells, orient cells to move in the right direction and at the speed needed to heal wounds, much like a Global Positioning System helps ships navigate to their destinations.

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What we are dealing with is a physiological analogy to the GPS system with a coupled autopilot that coordinates air traffic or tankers on open sea," says Soren T. Christensen, describing his recent research findings on the primary cilium, the GPS-like cell structure, at the American Society for Cell Biology (ASCB) 48th Annual Meeting, Dec. 13-17, 2008 in San Francisco. Christensen and his colleagues at the University of Copenhagen in Denmark and the Albert Einstein School of Medicine in the Bronx studied the primary cilia in lab cultures of mice fibroblasts, the cells that along with related connective tissues sculpt the bulk of the mammalian body.

So we think we have designed GPS systems?

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"The really important discovery is that the primary cilium detects signals, which tell the cells to engage their compass reading and move in the right direction to close the wound," Christensen explains.

Purposefully communicating information as a means to an end... wound healing.

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The researchers suspect this cellular GPS system plays roles other than wound healing. The primary cilia could serve as a fail-safe device against uncontrolled cell movement, says Christensen. Without chemical stimulation, the primary cilia would restrain cell migration, preventing the dangerous displacement of cells that is associated with invasive cancers and fibrosis, the scientists explain. On the other hand, defective primary cilia might fail to provide correct directional instructions during cell differentiation. This failure could be another link connecting primary cilia to severe developmental disorders, the researchers suggest. Protruding through the cell membrane, primary cilia occur on almost every non-dividing cell in the body. Once written off as a vestigial organelle discarded in the evolutionary dust, primary cilia in the last decade have risen to prominence as a vital cellular sensor at the root of a wide range of health disorders, from polycystic kidney disease to cancer to left-right anatomical abnormalities.

Demonstrating the vacuity of preaching sub-optimal design... an idea from faulty Darwinian reasoning?

And taking clues from original design (cellular machinery) to design our own optimal nanotechnology? Does that make the original design optimal/above par/good?

Clockwork That Drives Powerful Virus Nanomotor Discovered

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Because of the motor's strength--to scale, twice that of an automobile--the new findings could inspire engineers designing sophisticated nanomachines. In addition, because a number of virus types may possess a similar motor, including the virus that causes herpes, the results may also assist pharmaceutical companies developing methods to sabotage virus machinery.

Related article:
Biologists Learn Structure, Mechanism Of Powerful 'Molecular Motor' In Virus

One has to wonder were the next spate of these arguments are going to come from? Perhaps the low optimality of the genetic code? Perhaps not... Maybe the inefficiency of biomolecular machines? Maybe not...

Arguments from bad design should be taken with a pinch of salt as they are often made out of ignorance with hidden meaningless and mindless metaphysical propositions.

White blood cells, catapults, DNA repair and junk DNAnomore

White Blood Cell Uses DNA 'Catapult' To Fight Infection

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U.S. and Swiss scientists have made a breakthrough in understanding how a type of white blood cell called the eosinophil may help the body to fight bacterial infections in the digestive tract, according to research published online in Nature Medicine.

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Hans-Uwe Simon, from the University of Bern, Switzerland, Gerald J.Gleich, M.D., from the University of Utah School of Medicine, and their colleagues discovered that bacteria can activate eosinophils to release mitochondrial DNA in a catapult-like fashion to create a net that captures and kills bacteria.

Dang, how cool is that. Like catching fish (bacteria) with a DNA net.

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"This is a fascinating finding," says Gleich, professor of dermatology and internal medicine at the University of Utah and a co-author of the study. "The DNA is released out of the cell in less than a second." Eosiniphils, which comprise only 1 to 3 percent of human white blood cells, are known to be useful in the body's defense mechanisms against parasites. But their exact role in the immune system is not clear. Unlike other white blood cells, which are distributed throughout the body, eosinophils are found only in selected areas, including the digestive tract. Mitochondria – often referred to as the power plants of the cell – are components within cells that are thought to descend from ancient bacteria. Although most cellular DNA is contained in the nucleus, mitochondria have their own DNA.

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The researchers hope to learn more about how eosiniphils expel mitochondrial DNA. They speculate that the explosive mechanism might rely on stored energy, similar to the way plants release pollen into the air. "We don't know how eosinophils are capable of catapulting mitochondrial DNA so quickly," says Gleich. Future investigation may focus on how this energy is generated and how this new knowledge can be applied to the treatment of bacterial infections and inflammatory diseases related to eosinophils.

More functions for previously thought Darwinian junk DNA.
How DNA Repairs Can Reshape Genome, Spawn New Species

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Researchers at Duke University Medical Center and at the National Institute of Environmental Health Sciences (NIEHS) have shown how broken sections of chromosomes can recombine to change genomes and spawn new species.

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"People have discovered high levels of repeated sequences in the genomes of most higher species and spun theories about why there are so many repeats," said Lucas Argueso, Ph.D., a research scholar in Duke's Department of Molecular Genetics and Microbiology. "We have been able to show with yeast that these repeated sequences allow the formation of new types of chromosomes (chromosome aberrations), and represent one important way of diversifying the genome." The scientists used X-rays to break yeast chromosomes, and then studied how the damage was repaired. Most of the chromosome aberrations they identified resulted from interactions between repeated DNA sequences located on different chromosomes rather than from a simple re-joining of the broken ends on the same chromosome. Chromosome aberrations are a change in the normal chromosome complement because of deletion, duplication, or rearrangement of genetic material. On rare occasions, the development of one of these new chromosome structures is beneficial, but more often DNA changes can be detrimental, leading to problems like tumors. "Every so often the rearrangements may be advantageous," Argueso said. "Those particular differences may prove to be more successful in natural selection and eventually you may get a new species.

Repeat sequences aid in chromosome aberration repair and contributes to introduction of variability.




Look at all that Darwinian junk in the genome, honestly, who would make such a useless genome.
But, but, but....
'Junk' DNA May Have Important Role In Gene Regulation

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ScienceDaily (Oct. 20, 2008) — For about 15 years, scientists have known that certain "junk" DNA -- repetitive DNA segments previously thought to have no function -- could evolve into exons, which are the building blocks for protein-coding genes in higher organisms like animals and plants. Now, a University of Iowa study has found evidence that a significant number of exons created from junk DNA seem to play a role in gene regulation.

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"Hundreds of exons in the human genome were created from Alu elements. The whole-genome exon microarray allowed us to quickly identify exons that most likely contribute to the regulation of gene expression and function," said Lan Lin, Ph.D., University of Iowa postdoctoral fellow in internal medicine and the lead author of this study. Analysis of one human gene, SEPN1, which is known to be involved in a type of muscular dystrophy, along with comparative data from chimpanzee and macaque tissues, suggested that the presence of a muscle-specific Alu-derived exon resulted from a human-specific change that occurred after humans and chimpanzees diverged evolutionarily. "In this case, this exon is only expressed at a high level in the human muscle but not in any other human or non-human primate tissue, so this implies that the exon plays a functional role in muscle, and this role is human-specific," said Xing, who is also affiliated with University of Iowa Center for Bioinformatics and Computational Biology.

... you forget about cellular intelligence capable of harnessing random variation and selection.