Point 1:
Since scientists learned how to "read" the whole genome in the 1990s, they discovered a large percentage of species' genes are not related to any other lineage. At first they thought the lineages would fill in as they did more sequencing, but they eventually realized the genes did not all follow the neo-Darwinian theory. These particular ones are called Orphan, or ORFan, genes. The Orphans show up at a rate of at least 10-30% in all lineages. Wikipedia has an article about Orphans HERE. (If you read this or any other article about biology, beware that the evolution theory is usually assumed as proven. So just try to get the actual facts.) The abstract of this artice by Arendsee, Li and Wurtele, "Coming of Age: orphan genes in plants," Trends in Plant Science 19, 11 (Nov. 2014): 698-708, also speaks of orphans in all species.
Point 2:
So because Orphans became part of the overall picture, scientists are looking for other ways to justify evolution. Before, they said small mutations in genes over billions of years would bring the changes we see in species and beyond, all through life's varieties. So now they are telling us the reasons genes are not following trees is that various major mutations and duplications can happen within the non-functional part of the genome, or they go from one species to another by what is called horizontal gene transfer (HGT). I will take HGT under Point 3.
But experiments over the last 30 years have shown that functional proteins are very rare. Among the papers describing this rarity is by JF Reidhaar-Olson and RT Sauer, "Functionally acceptable substitutions in two alpha-helical regions of lambda repressor," Proteins, 7, 4 (1990): 306-16. When similar experimental results are considered, we can use the proportion of 1 in 10^70 as a guideline for function of a simple protein "fold." Folds are the parts of proteins which react with other biochemicals to process our metabolism.
It has been estimated that less than 10^50 organisms could have been alive on Earth. This was done, among others, by Fredric P. Nelson, “Needed: A New Vocabulary for Understanding Evolution,” Perspectives on Science and Christian Faith 58, 1 (March 2006): 28-36.
Bacteria have less than one mutation per generation. Even in billions of years, there were not enough organisms to bring about millions of unique, Orphan genes to functional structure (there are estimated to be about 10 million species on Earth). This is not even to mention the continuing discoveries that more of the "non-functional" part of the DNA is in fact useful for a variety of reasons and probably not available for mutation.
Point 3
Horizontal gene transfer is an exchange of DNA between species. The sets of proteins used in HGT, along with other functions,including the secretion of toxins, are know as "secretion systems." There are various types, and I have images of one part of a Type II and full Type IVa machine. There are good images and information of both of these systems online in a scientific article by Chen and Dubnau, "DNA uptake during bacterial transformation," Nature Reviews Microbiology 2, 3 (April 2004): 241-249.
Information about this process has been studied and the following facts are from an article by Thomas and Nielsen, "Mechanisms of, and barriers to, horizontal gene transfer between bacteria," Nature Reviews Microbiology 3, 9 (October 2005): 711-721. Although HGT does work at the single-celled organism level, most changes are deleterious. Of the few that do persevere and spread, they are most often involved in simpler biochemical pathways, even in antibiotic resistance. They do not affect the most central workings of the cell, such as DNA replication. Even so, it takes about 20-50 already functional, coordinated proteins to perform HGT.
Scientists and others have used these systems as examples of evolutionary sources for the bacterial flagellum system, which in turn is a model of design given by Intelligent Design advocates. But the anti-design scientists don't explain how the proteins of these systems arose and organized into working machines of their own.
Type II Secretion System
The first image is one protein of a Type II secretion system. It is from the work of Abendroth et al., "The X-ray Structure of the Type II Secretion System Complex Formed by by the N-terminal Domain of EpsE and the Cytoplasmic Domain of EpsL of Vibrio cholerae," Journal of Molecular Biology 348, 4 (May 13, 2005): 845-855. The protein is called Cyto-Epsi," and the PubMed Abstract in part describes it:
Gram-negative bacteria use type II secretion systems for the transport of virulence factors and hydrolytic enzymes through the outer membrane. These sophisticated multi-protein complexes reach from the pore in the outer membrane via the pseudopilins in the periplasm and a multi-protein inner-membrane sub-complex, to an ATPase in the cytoplasm.
The image shows a protein that has one type of chain with 254 amino acids, but it is a 2-mer, which means there are two of the same type in the molecule, totaling 408 amino acids. Amino acids are the subunits of proteins and have an average of about 20 atoms. The double chains of the 2-mer are apparent from the mirror-type image. Remember, this is just part of the system.
More information, including the journal abstract, about Cyto-Epsi from Type II can be found at RCSB PDB 1YF5.
More information on Type II secretion systems at Wikipedia HERE.
Type IVa Secretion System
The second image is a Type IVa secretion system (piliated, which means the center has a separate protein string that the system made). The journal article which describes this is by Chang, et al., "Architectural model of the type IVa pilus machine," Science 351, 6278 (March 11, 2016): aad2001. The full Science article is online with images at the link in the title.
This image of the Type IVa Pilus Machine is from Uniprot, another protein database. It is pictured at the links to the individual proteins that make up the machine. For example, one of the proteins is called PilB, and when you go to Uniprot PilB entry (with the right browser setup) you get this image. It is under the heading "Structure" and you can even manipulate the 3-D image! Give it a try at PilB entry Q1D098. Once again, this machine is not the whole system.
More information about the Type IVa pilus machine is at RCSB PDB 3JC8.
At the RCSB PDB 3JC8 link, there are Protein Feature view charts for each of the 9 types of proteins that make up this particular machine. The third image here is the Type IVa pilus assembly protein ATPase PilB from the organism, Myxococcus xanthus (strain DK 1622). The 9 types of proteins (entities) have multiple chains of each. In this example, PilB has 566 amino acids in each of 6 chains (the blue lines).
The amino acid sequence of PilB is what each of the blue lines represent. This particular one is shown here from the Uniprot website, each letter standing for a specific amino acid:
The total amino acids (also called residues) for this machine are listed at the site as: 37,468. Total atoms: 107,640. All have to interact in size, shape and charges for the machine to be in working order.
More on Type IV Secretion Systems at Wikipedia HERE.
If you've gotten to this point, thanks for following along. I hope you see these systems are themselves intricate, not easily explained away.
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