Biological Evidence Against Intelligent Design

This falsifies ID according to your criteria:"To falsify intelligent design, you have to find an unambiguous example of natural causes that would show how life or the flagellum was generated."--traderdrew, message 205

You tell me. It is IDists who claim that the flagellum could not have evolved through successive steps. So please show us the bacterial generation just prior to and just after the appearance of the flagellum and demonstrate that the change from one generation to the next was not due to evolution. So how did they discover these things? They used their five senses to discover these things, did they not? How else does one observe the results of the double slit experiment if not with their eyes? How else does one observe the paths of sub-atomic particles through a cloud chamber if not with their eyes? You can even use your ears to listen to the cosmic microwave background on a radio.

It appears that you can't see it either. If you did see it you would explain it.

The key to the past is the present. How do bacteria do it now?

quote:

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The major subunit FliC and the minor subunits FliD, FlgK, and FlgL are delivered from the cytosol to the base of the nascent flagellum by a type III export pathway in which they are bound by the subunit-specific export chaperones FliS (for FliC), FliT (for FliD), and FlgN (for FlgK and FlgL). These export chaperones effect transition to the membrane by preventing premature polymerization of subunits, acting as bodyguards for the C-terminal amphipathic oligomerization domain (2—4) and by piloting the subunits to the export apparatus (5).
Lewis et al. 2006

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Chaperone proteins can also be found for the toxins associated with the TTSS. I don't know. Why don't you show me the math. The part of natural selection that always selects for function that benefits the organism. Again, why don't you show us the math and the assumptions used in calculating the probability.Frankly, I think it is nearly impossible to calculate these odds. First, you need the target which must describe ALL proteins that would have resulted in some sort of motility system. Mind you, the target is not what did evolve but the total list of all proteins that COULD HAVE evolved into a motility system. How do we do that? Given the trillions and trillions of possible proteins it is impossible to test all of them for their potential in a motility system.Also, these proteins must be tested against the genetic background of the pre-flagellar genomes of bacteria. We don't have those genomes, or really a strong idea of what they looked like. The same function that the TTSS has now outside of exporting flagellar proteins. It delivers bacterial toxins that kill eukaryotic cells. In some lineages the toxin secretion function was kept. In some lineages the flagellar function was kept. In some lineages both functions were kept.You are making the fallacious "if men evolved from apes why are there still apes" argument.

Just for some background, these experiments were done to help understand why some genes were difficult to sequence. When a genome is sequenced the first step is to break up the genome into smaller chunks, usually through digestion with endonucleases. These smaller chunks are then inserted into plasmids. The E. coli are used to house these plasmids. If one of the genes in the inserted plasmid is toxic to the E. coli then you will not get a viable clone for this piece of the genome that is being sequenced. The authors of this paper wanted to figure out why these specific chunks of DNA could not be sequenced using this technique. As it turns out, these genes have active promoters that E. coli recognizes and the resulting protein and/or mRNA is toxic to the E. coli.So the DNA transfers just fine. E. coli take up exogenous DNA very readily which is one reason why the are used extensively in laboratories. Like I said above, the DNA gets in just fine. I didn't see any specific details for their protocols but from my experience the antibiotics and IPTG had nothing to do with the actual transfer of the DNA. What they probably did was use a plasmid carrying the lacZ promoter and an antibiotic resistance gene. The antibiotic resistance allows them to screen for clones that have the plasmid, and the IPTG (a lactose sugar analog) activates the lazZ promoter allowing for controlled expression of the gene inserted into the plasmid. This allows them to clone toxic genes under control of the lacZ promoter instead of the promoter that is associated with the gene in the original host. This is a very common plasmid used to express recombinant proteins in E. coli. Using this set up they were able to show that the genes do get into the cells but that expression of these genes results in toxicity.On top of that, only a few of the genes considered were untransferable"We considered only genes 1.5kb or less (246,045 genes, representing 85% of all annotated genes), as larger genes are less likely to be covered to their full length by multiple clones.

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Of the genes inspected, we recorded 1,402 instances (642 different genes) in which a gene with a Clusters of Orthologous Groups (COG) annotation was not fully represented in any single clone, and was marked as untransferable to E. coli (with an estimated false positive prediction rate of 0.9%-1.3%; see SOM)."So it would appear that less than 1% of genes (1,402 out of 246,045 genes of 1.5k bases or larger) are toxic when transferred into E. coli. They then show that the homologs of an untransferable gene in closely related species are likewise untransferable which isn't too surprising.Edited by Taq, : No reason given.

Then let's look at what HGT can do. It can transfer functional proteins that work in one species into another species. When these proteins find themselves in a new species they may very well bind to different proteins and take on new roles in the new species.Think of it in terms of human technology. There was no need for hundreds of different cultures to independently invent the wheel. Instead, a single culture invents the wheel and then that invention is horizontally transferred to other cultures when they come into contact.

Passing genes from one generation to the next is VGT, or vertical genetic transfer. These terms come from the "tree of life" metaphor for the organization of species. Vertical transfer goes up the branch. Horizontal transfer occurs across the branches, between species.In metazoans like us HGT occurs very rarely. This can include movement of DNA from your mitochondria into your nuclear genome (called numts) or by insertion of exogenous retroviruses resulting in endogenous retroviruses (called ERV's). But as you can already guess it is very difficult for DNA from say modern bears to make its way into the modern primate branch.In bacteria it happens quite readily. In fact, "species" is a bit hazy for bacteria given that bacteria can easily conjugate (using sex pilli) between species. Also, bacteriophage (the bacterial version of retroviruses) can pull along chunks of host genome and insert it into other bacterial species. Because of HGT it is very difficult to resolve a single tree for all bacteria.

Didn't anyone give you the talk about the birds and the bees?