Examples of incompetent/sadistic design

[The Emu's Prophet]

I thought it might be fun to have a thread on examples of 'design' which contrary to being indications of intelligence, could only be the handwork of a designer that is stupid and/or evil.

One example that struck me during my revision for my biochem exam is that of cytosine methylation.

In DNA, three of the four bases used to code for proteins, cytosine, adenine and guanine all contain NH2 groups, which can at any time be spontaneously lost through hydrolysis. This will cause them to be converted to a different base - cytosine will become uracil, guanine will become xanthine and adenine will become hypoxanthine. This has the potential to lead to mutations, as the basepairing will be altered - while cytosine will pair with guanine, its deamination product, uracil, will pair with cytosine. Likewise, xanthine pairs with thymine while its progenitor guanine pairs with cytosine, and hypoxanthine pairs with cytosine vs thymine in the case of its progenitor, adenine. This will cause problems in DNA replication, as the altered base pairing properties will mean that the wrong complementary base will be placed on the opposite strand, leading to a point mutation. However, mutations can often be averted, because none of the bases produced by deamination are normally present in DNA. As such, it is possible to unambiguously recognise them as foreign bases that should not be there, remove them, and replace them with the correct base. If this is done before the DNA replicates, no mutation will occur.

This is the reason why unlike RNA, DNA does not use uracil, and uses thymine instead. Thymine is identical in structure to uracil, except with an added methyl group, which makes it possible to distinguish between the methyluracil, which is supposed to be there, and ordinary uracil which is a product of cytosine deamination, and needs repairing. So, having established this system of avoiding mutations caused by base deamination, what mindbogglingly stupid innovation did nature decide to use to stuff this up? The answer is cytosine methylation. Nature thought that it would be a really cool idea to introduce methods of gene regulation that work by tagging cytosine with a methyl group in the 5 position. The tiny little drawback to this idea is that while ordinary cytosine will deaminate to uracil, methylcytosine will deaminate to methyluracil - i.e. thymine. Because thymine is not foreign to DNA, any thymine produced by the deamination of methylcytosine cannot be selectively removed and replaced, as it is indistinguishable from the thymine that's supposed to be there. As such, the use of cytosine methylation to regulate cell function is simply asking for mutations, and all the problems that go with them (like cancer). Of all the possible ways of labelling cytosine, using one that allows cytosine transform into a normal base, making it impossible to tell the difference between the damaged form of it and a base that's supposed to be there, could only be considered moronic if a being designed things to work that way. The use of any other funtional group as a 'tag' for cytosine would have averted this problem, meaning that any designer with even the slightest idea of what it was doing could have easily created a means of tagging cytosine that doesn't lead to mutations.

[Hueglow]

There's always the centuries-old argument that God did it to punish us. It would be strange to do that by inventing a device that can lead to the death of millions of people regardless of their moral behavior (or anything that God would judge) when He could have created several other methods. Or he could just kill the evil people straight away, which he has literally no difficulty in doing; it would be much more efficient and sometimes could even benefit good people who would become victims of the evil.

Other explanations that I can imagine, based on what I've heard from some Christians sometime, is that God did these things to make the world a more interesting place, or that evil is necessary for good to exist (presumably so they'll contrast, making them clearer to our eyes). But these ideas are focused on human traits, which God created out of his own will - unless if people are like that to mirror God, but I find it improbable that those characteristics (like needing to see problems to have an interesting life) are in God's essence, which would mean that they precede the very existence of the world. (That would at least explain why he created the world (a question that is seldom posed): he found it too boring the way it was before.)

I don't think a perfect designer would have created viruses either. I can think of only two explanations: the one I mentioned earlier, about punishing the people He created by killing some of them randomly, and that He created them as a way to promote natural selection. I'm not a biologist, but, as far as my knowledge goes, the benefit of being selected by viruses would be becoming resistant against viruses. So that would be a pointless and tragic waste of time.

The final explanation I can give is that God let Evolution run without interference, and because of that some undesirable things happened. There can be an explanation for God's obsession for not interferring and not appearing, but it's out of our capacity of comprehension.
Nevertheless, Christian doctrine cleary teaches us that God created humans on purpose and has a plan for everything; if he created humans on purpose through Evolution, I can't see why the much earlier creation of viruses wouldn't have been on purpose either. 

(I know "Intelligent Design" supporters are people who don't believe in Evolution, but most other Christians who accept Evolution also believe that God designed everything with perfection and harmony.)

[Gnomon]

The use of any other funtional group as a 'tag' for cytosine  would have averted this problem, meaning that any designer with even the  slightest idea of what it was doing could have easily created a means  of tagging cytosine that doesn't lead to mutations.

On the other hand, you might attribute this little "glitch" to a clever designer*, who wanted to allow random changes in an otherwise Xerox reproduction process. Without occasional mutations, there would be no humans to criticize the imperfect design---only gene-swapping bacteria.

* In the sense of "design" by evolutionary algorithms.

Wiki :
The genetic algorithm (GA) is a search heuristic that mimics the process of natural  evolution. This heuristic is routinely used to generate useful solutions  to optimization and searchproblems. Genetic algorithms belong to the larger  class of evolutionary algorithms (EA), which  generate solutions to optimization problems using techniques inspired by  natural evolution, such as inheritance,  mutation, selection, and crossover.

[Gurra100]

There are some fantastic "biblical solutions" to this.

In the garden of Eden the "tag" for cytosine was probably different, and harmless. But then the innocent  humans in a confused moment, was lured by the furocious snake (really the devil in disguise) to eat that cursed apple, and soon became aware and ashamed of that they were naked.  This loonecy might  indicate that this apple caused a genetical change of the DNA and probably also changed the "tag" for cytosine. You are what you eat!

("The tree of knowledge of good and evil" might have been an ironical  name. Why should anyone want to distinguish between god and evil when  there is a possibility to live a life almost completely free from evil  without even thinking about it.? Also note that the name of this tree was not "The tree of knowledge" only. So there was generally nothing wrong with knowledge in the Garden of Eden. It migth have been a stimulating place. Sex and gardening and a little chat with the animals now and then. )

So this version puts the blame on the Devil.

The other version I am considering is that this genetical transformation was a part of the punishment distributed by God when he found out about that apple. He was never that pissed before !!

Well somebody did it anyway !

I don´t believe in the Bible by the way. I only happen to like some parts of it !

[The Emu's Prophet]

There's always the centuries-old argument that God did it to punish us. It would be strange to do that by inventing a device that can lead to the death of millions of people regardless of their moral behavior (or anything that God would judge) when He could have created several other methods.

Such a possibility would come under the 'malevolent designer' label.

I don't think a perfect designer would have created viruses either. I can think of only two explanations: the one I mentioned earlier, about punishing the people He created by killing some of them randomly, and that He created them as a way to promote natural selection. I'm not a biologist, but, as far as my knowledge goes, the benefit of being selected by viruses would be becoming resistant against viruses. So that would be a pointless and tragic waste of time.

Actually, viruses need not be necessarily bad. Viruses are effectively pieces of genetic code which are capable of travelling from cell to cell. They are thought to have descended from transposons, which are genes which are capable of moving from one location on a genome to another, and also of making copies of themselves within the genome. They serve no useful function to the organism, and in fact are harmful - if they insert themselves in the middle of a useful gene, then that gene will be interrupted and no longer function, and can cause cancer should they inactivate tumour suppressor genes in this way. They continue to exist simply because they are good at replicating, even if they are detrimental to the organism as a whole. Viruses, then, are simply transposons which have managed to evolve mechanisms to insert themselves into the genomes of other cells. As viruses are effectively mobile genetic information, it is possible that they can bring with them genes which are actually beneficial; for instance they could give the cell the capacity to synthesise a new, useful protein. I'm not sure how common symbiotic viruses are, but they are very important drivers of evolution; if I recall, around about 8% of our genome originated from viruses, with some of those genes being coopted to perform useful functions. Viruses provide a means by which genetic information can be exchanged between organisms, even ones of different species - sometimes when a retrovirus replicates, it will also carry with it neighbouring genes from the host genome. These can then be incorporated in the genome of another organism when it gets infected by the virus.

Also, from a human perspective, viruses are likely to become an important tool of medicine in the future, as they represent an easy way of transporting genetic information into cells.

Still, there would be no need for them if organisms were perfectly designed to begin with. And, even if the designers did have need of them, because for whatever reason they weren't capable of creating perfect organisms from the get go, why are the vast majority of viruses harmful? If the creators were truly benevolent, the only viruses we would be likely to encounter would be ones specially designed by the creators to make improvements to organisms, not kill them in a variety of unpleasant ways.

On the other hand, you might attribute this little "glitch" to a clever designer*, who wanted to allow random changes in an otherwise Xerox reproduction process. Without occasional mutations, there would be no humans to criticize the imperfect design---only gene-swapping bacteria.

Using an evolutionary method is only necessary for designers of limited means - very limited indeed when you consider how inefficient evolution is as a process. An intelligent designer of unlimited means would have no need for mutation at all, and would strive to make mutations impossible - since they could create perfect entities ex-nihilo, any change would be for the worse. Furthermore, even if we assume the existence of creators who are of such limited means that the only method they have access to is evolution, it does not make the use of cytosine methylation as a means of gene regulation any less clumsy. While it is necessary for mutations to take place in order for evolution to occur, this is only of use if they take place in germline cells. Somatic cell mutations are useless. Even if a beneficial mutation does occur in a somatic cell, it is likely to be of no benefit to the organism. The best you're likely to get is a small colony of a few thousand liver cells which can make a better enzyme, which is too few to be of any use, or a minescule patch of skin which is slightly more resistant to skin cancer. And these improvements, as they are not passed on, will die with the organism. On the other hand, a detrimental mutation in a somatic cell can be catastrophic. If a mutation removes the capacity of a cell to control its rate of replication, cancer is the result. Using a mutagentic means of gene regulation like cytosine methylation to introduce new mutations into a gene pool is clumsy and inefficient, as for every one mutation produced in a germline cell, there will be billions of pointless mutations occuring in somatic cells which pose a hazard to the organism. If a benevolent and intelligent designer really wanted to introduce mutations, it would be well within their power to introduce a method of controlled mutation which only takes place in germline cells, rather than one which produces increased rates of cancer and loss of cell funtion as an inevitable consequence of it in every organism in which it is implemented..

[Zoon van Ijs]

 I found this video just today.. it has some examples of "design" flaws..     

[nom]

I found this video just today.. it has some examples of "design" flaws..    

Link?

[Zoon van Ijs]

I found this video just today.. it has some examples of "design" flaws..     

Link?

  Weird!!  I'm like 200% sure I posted the link... 

Here it is anyway: http://www.youtube.com/watch?v=Lcrq5OOkQdk

 Is it still there? 

[nom]

I found this video just today.. it has some examples of "design" flaws..     

Link?

  Weird!!  I'm like 200% sure I posted the link... 

Here it is anyway: http://www.youtube.com/watch?v=Lcrq5OOkQdk

 Is it still there? 

  design!