To understand the theory of evolution and universal common descent I have been told to read biology textbooks. The funny part is that every time I do so the design inference is confirmed.
The following is what one gets when one reads biology textbooks (quotes are from Bioinformatics, Genomics, and Proteomics: Getting the Big Picture
by Ann Finney Batiza, PhD, which is part of a series- "Biotechnology in the 21st Century"):
It is important to note that the proteins made by an organism determine all of the characteristics that “nature” provides for that particular living thing. The enzymes allow other molecules, including proteins, fats, and carbohydrates to undergo chemical reactions, such as being put together or taken apart inside living things.
… (skipping surface receptors and other structural elements)
Other proteins bind DNA, the molecules of heredity, and determine which codes are going to be used to make proteins- at which time and in which type of cell.
Because each protein has an important job to do, it is crucial that proteins be made to precise specifications, just like the precision parts of an expensive sports car. In fact, the blueprints for some proteins have been so good, they have been preserved through millions and even billions of years of evolution.—page 5
However no one ever says how they evolved in the first place.
The importance of these precise structures and hence functioning of protein machines like these channels cannot be understated. Potassium channels, like other channels that pass other ions from one side of the cell membrane to the other, have a particular architecture that allows them to open and close upon command. We now know that intricately designed and mechanically fine-tuned ion channels determine the rhythm and allow an electrical impulse initiated when we stub our toe to be transmitted to the brain.- page 19
Wet electricity. Whereas the electricity that powers our computers is comes from the flow of electrons through a conductor and “hates” water, the electricity that runs our bodies is designed for a wet environment and uses pumped ions to convey differing messages to our command center.
Those magical mystery mutations are pretty powerful stuff!!
But wait, there's more!
Just for a eukaryotic cell to make an amino acid (polypeptide) chain-
Transcription and Translation-
You start with a tightly wound piece of DNA. Enzymes called RNA polymerases, along with other transcription factors, begin the process by unwinding a portion of DNA near the start of a gene, which is specified by sequences called promoters. Now there are two strands exposed. One strand is the coding strand- it has the correct sequence information for the product- and the other strand is the non-coding strand. That strand contains the complimentary layout.
At this point decisions have to be made. Where to start, where to stop and although it may seem counterintuitive the mRNA goes to the non-coding strand in order to reconstruct the proper codon sequence (nucleotide triplets which code for an amino acid) for the protein to be formed. Both sides of the parent DNA are exposed yet the mRNA "knows" to only form on one.
This process is unidirectional (5’-3’). There is only one start codon which also codes for an amino acid (met) and therefore all amino acid sequences start with methionine. The stop codons don’t code for an amino acid. Transcription actually starts before the “start” codon and continues past the stop codon. Before the mRNA leaves the nucleus any/ all introns are cut out and the remaining exons spliced together. A chemical cap is added to the 5’ end, the non-coding stuff at the end is cut off by a special enzyme (endonuclease) and a string of A’s is added in its place. You now have a processed mRNA.
So now we have this piece of processed mRNA which leaves the nucleus and has to rendezvous with a ribosome-the protein factory within the cell. On to translation
A ribosome consists of over 50 proteins and 3-4 different kinds of rRNA (ribosomal), plus free-floating tRNA (transfer). Each tRNA has a 3 nucleotide sequence- the anti-codon to the mRNA’s codon plus it carries the appropriate amino acid molecule for its anti-codon. To attach the appropriate amino acid to the correct anti-codon an enzyme called amino-acid synthetase is used.
There, large workbenches made of both protein and nucleic acid grab the mRNA so the correct amino acids can be brought up to the mRNA. Each amino acid is escorted by a module called tRNA or transfer RNA. It is important to note that the escort molecules have three bases prominently exposed on their backsides and that these molecules also use the base U instead of T. The kind of amino acid is determined precisely by the tRNA escort’s anticodon, or triplet set of bases on the escort’s backside.-pg 23
And then the chain starts forming until the stop codon terminates the process.
Next is the folding process. That is what allows the protein to be useful- its spatial configuration.
That is just the basics of what one is introduced to when reading biology textbooks. And it doesn't include the proof-reading and error correction
that accompanies the process.
So the bottom-line is if biology textbooks got rid of the biased, untestable and unscientific leanings toward non-telic evolution students reading the books would come to the design inference just based on the data.
None of that "just happens". Purely artificial ribosomes do NOT work. They would work if they were reducible to their physical parts, so that means there is something missing. That something is software.