Preaching sub-optimal design: An argument from ignorance?

General Academics Religion and Philosophy
1

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 gicen by Richard Dawkins. Take his article:
The Information Challenge

[b]Genomes are littered with [u]nonfunctional pseudogenes[/u], 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. [u]And there's lots more DNA that doesn't even deserve the name pseudogene.[/u][/b] It, too, is derived by duplication, but not duplication of functional genes. [u]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.[/u]

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

"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

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

ScienceDaily (Oct. 20, 2008) — For about 15 years, scientists have known that certain "junk" DNA -- [b]repetitive DNA segments previously thought to have no function [/b]-- 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. :mrgreen:

And what crackpot theory suggested the appendix is useless and functionless.

A few articles indicating 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.
  6. Appendix May Actually Have a Purpose

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…

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Continued:
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). What crackpot theory suggested that? Seems like pretty high-tech structures to me?

Primary Cilium As Cellular ‘GPS System’ Crucial To Wound Repair

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.
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?

"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.

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.

One has to wonder were the next spate of these poorly thought out 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.

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Very interesting, indeed! Once again, the scientific method proves its worth by showing new evidence suggesting that certain things aren’t quite as clear-cut as was previously thought. If these findings prove out, the relevant body of science will be suitably amended to accommodate them.

As for bad “designs,” here’s an article that considers the human body with particular reference to longevity (which in itself has no evolutionary advantage – quite the opposite, actually, when viewed from the species perspective).

'Luthon64

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Over the years many people have come with arguments that systems in nature are sub-optimal, or sub-par.

Calling biological systems “sub-par” or “sub-optimal” is absurd. I believe that these terms rely on notions of absolute ideals, or standards, and as such cannot be applied to biological systems.

(Just a note on the term “system”. In its usual physiological sense, I understand “system” to mean a group of organs that work together to perform a certain task. The cardiovascular “system” features heart muscle, veins and capillaries, and its function is to deliver oxygen and nutrients, and to remove carbon dioxide and waste from somatic cells. But I see no reason why a “system” can’t also refer to the haemoglobin alone, which seems to exist for the sole purpose of repeatedly binding and liberating oxygen. Similarly, an iron ion within the haeme moiety may perhaps also be viewed as a system, its function being to donate and accept electron density on demand. The point is that an organism may be divided into as many subjective systems as you care to define. In the context of this thread, can we simply let “system” mean any biological feature that has at least one function.)

From the Wiktionary, “par” means equality of nominal and actual value, while “optimal” means the best, most favourable or desirable, especially under some restriction.

A system runs the risk of being criticized as being sub-optimal or sub-par if the system is perceived as ineffective or wasteful. (The eye-criticism falls in the first group, the junk-DNA-crit in the second.)

How does the critic support her contention? She must have evaluated the quality of the system by comparing it against a nominal value, or standard. But what is this standard? I can think of only two standards available to the critic of systems. The first standard is imaginary, the second is real.

The problem with imaginary standards is that they are rubbish. Spotting a goat struggling to reach a pear on an overhanging branch, you can say :”A-ha! That goat needed longer legs. A clear sub-optimal design.” But you will neglect for the fact that the goat also needs sturdy legs when climbing rocks to reach its water supply. We can’t possibly take into account the full sum of constraints that a system has to cope with, so our imaginary standard will simply not apply to real systems. Apples and oranges.

That leaves real standards. The only option here is to compare the offending system to an equivalent system in another species. So the standard now becomes any arbitrary system in the set of interspecific analogous systems. To refute by example, consider a member of the mammalian dental arch. The function of the canines are tearing, protection and conveying threats. As such, the human canines scarcely compare to those of even the smallest house cat. Are our canines therefore sub-par? Are those of the cat sub-par compared to that of the lion? Moreover, will little Moggy be better off sporting the full length sabers of its famous prehistoric relative? What works “better” for one species, will not always work “better” for another. This leaves us without any easy criterion for selecting the standard. So interspecific system comparisons, are also nonsensical.

Still, the idea of fitness of one form relative to the next is required as a driver for natural selection. The fitness of a form depends on the sum of the quality of its systems, and as such I think we can only ever comment on one individual’s fitness relative to another after the fact, i.e. when one form becomes out-competed and extinct.

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I hope you will forgive me for making my first post as a newbie on this forum a rather directed response both at the original post, and to some extent at the original poster - the reason will become clear.

The concept of “sub-optimal design” or “poor design” has been used mainly in two ways. Firstly as an argument against the existence of a creator-god ( for fairly obvious reasons ), and secondly as an argument against the idea of “intelligent design” a.k.a. “creationism”. The first part of the topic subject - “Preaching sub-optimal design” - gives a clue that we are actually dealing with one of these two.

The Intelligent Design movement promotes an active effort on the part of its followers to attack evolutionary theory, to discredit the theory of evolution, and to subvert scientific evolutionary thinking. Large amounts of money and resources have been used to forward these goals and provide material for I.D. followers - the “Teach the Controversy” campaign by the Discovery Institute being one example. So the movement is active, and in a sense evangelical - I.D. must be preached and sold, scientific theories must be discredited and undermined in the process.

So please be warned, and beware of and skeptical about what Mechanist posts, as he posts almost exactly the same posts ( as for example his post here in this topic ) on other forums, in order to promote and defend Intelligent Design. As proof:

http://mybroadband.co.za/vb/showthread.php?t=151932

As to the original point about sub-optimal design, let me quote the most telling argument in the words of Will Provine, a Professor at Cornell University, to whose teachings I was ironically introduced by Mechanist himself:

The intelligent designer clearly is very short-sighted indeed. Virtually all of his creations are extinct.
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Some telling words:

Elsewhere:

'Luthon64

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And of course, is leaving out all the boring everyday things that ARE sub-optimal in the body, or sometimes downright broken…

People are born conjoined twins, with Down syndrome, with genetic predisposition to cancers, alzheimer’s, the list goes on… A LOT of people are born with under-sized jaws that don’t accommodate all their teeth. This often needs righting during adolescence (sometimes beyond) by a human doctor intervening and guiding the teeth to grow “correctly”, (Mintaka might not like my usage here, but I said it anyway) also often having to remove teeth. We need to remove a lot of children’s infected tonsils on a regular basis to stop the infections from becoming chronic and serious. Ag the list is almost endless, schizophrenia, retardation. In fact, I personally was born with a malformed kidney. I meant to use the singular, I only have one.

Some of these are simple flaws to be made by an all-powerful, all-knowing, perfect being. If you ask me this supposed creator sucks at design when your average dentist can do a better job.

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Sure enough, that’s all true. One must realise though that those constitute individual shortcomings whereas Jerry Coyne’s interest is in generic ones. That is, all normal human eyes (and those of many animals) suffer the same essential deficiencies. Individual defects like conjoined twins, Down’s syndrome, Alzheimer’s, etc., can be written off against an assortment of contrived adversities (not least of which is humanity’s sinful essence), but it is much harder to sweep generic flaws under the rug in the same way because they indicate fundamentally bad design rather than aberration, especially when they span across multiple species.

I think what this loaded question – “Preaching sub-optimal design: An argument from ignorance?” – is meant to convey is that the Intelligent Designer designed everything just the way it is for very good reasons that we are not presently aware of. In other words, everything in the universe is in actual fact optimally designed but our not being aware of the proper reasons for the chosen designs erroneously leads us to believe that the designs are suboptimal.

In the absence of those obscure-but-compelling reasons the aforesaid contention is, of course, undiluted rubbish because we can furnish sound reasons for judging the designs to be imperfect – seriously so in some instances.

'Luthon64

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Found a lovely site for you guys:
Some More of God’s Greatest Mistakes

I just wonder why these guys and you guys do not put the brain on that list?

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But the brain is suboptimal. That’s why IDiots and cretinists think it isn’t.

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Ah, at least one here that thinks brains, including his own, is a bit… suboptimal.
Guess you really have to be a believer to believe suboptimal brains can do anything that is not suboptimal.

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Your grammar, as apprehended by your brain, is suboptimal. Guess why.

Such as? Suboptimal ≠ wrong.

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Because you believe it is suboptimal…
Oh, your arguments and comments are a bit… suboptimal, since your brain (which you seem to believe is suboptimal) produce these “thoughts”.

Did your brain (that structure ou believe to be suboptimal) just burp out a suboptimal “musing”?

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No, because your suboptimal brain fucks up singular and plural.

No, it just did more work work than is strictly necessary to get there.

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Actually, anyone (me included) can give you the most perfect English grammar and understanding and you will still think it is suboptimal because you believe brains (the structures that produce English grammar and understanding) are suboptimal.

Looks like a bit of suboptimal work that is being done there by a suboptimal structure. You know, that structure you believe to be suboptimal. (hint hint, your brain)

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Now there you guys go again: slinging the word suboptimal around like it has any meaning in biology.

The body is a collection of those compromises that represent the best survival option under current selection pressures. If it wasn’t, it would be dead. I’d be very surprised if there exists any single organ that could be deemed as perfect by us after the fact.

Mintaka

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Well, all it does is show how Mecchie’s suboptimal brain confuses ideas and terminology (like “suboptimal” and “error prone”) 'cos it’s immovably fixated on this suboptimal idea that it’s the result of optimal design. In evidence, I offer his haphazard habit of making assorted suboptimal attributions and inferences as seen in his last three suboptimal posts.

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Guess describing the optimality of the genetic code has zero meaning to you?

Hey you are the one that believes brains are suboptimal. Don’t go thinking the above is anything more than suboptimal, you will only open yourself to cognitive dissonance.

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And you are the one with the suboptimal brain that thinks “suboptimal” means “flawed” or “unsound” instead of, say, “adequately serviceable”.

Whatever twiddles your suboptimal knobs for ya. Obviously on Mecchie-world a girder is “optimal” only if it can never fail under any load because it’s made of a completely indestructible material. ::slight_smile:

EDIT:

It doesn’t have any meaning in biology!? So I guess in biology a nerveless stump’s as good for manipulating objects as a hand with an opposable thumb, then. :o

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I must admit that I don’t see how one can make such bold subjective calls on any component of a living body. Unless you have a gift of foresight to such a degree that you can absolutely predict which parts of, say, the genetic code will survive into the distant evolutionary future, and which parts will be deleted. But I’m sure you will enlighten us. Incidently, where do you recon the genetic code is controlled, i.e. at what level is the code specified or dictated - DNA, mRNA, transcriptase?

The fact that the hand is better than the stump at grasping things does not imply that the hand is the best or even most optimal design, does it? How would the hand compare to one with even stronger or longer fingers? What exactly is this golden digitate standard against which you propose to measure the optimality of hand design?

Getting back to the stump. Unless the animal dies as a direct consequence of its stump, we cannot even comment on the stump’s optimality. Perhaps it is only ever used to crack open nuts, and any more subtlety in design would be an energy extravagance, soon to be punished by natural selection.

Mintaka