Detecting Design in a Biological Organism

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 conducter 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.


But wait, there's more!

Just for a eukaryotic cell to make an amino acid (polypeptide) chain-

Transcription and Translation-

Transcription:

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.

What that demonstrates is that it takes far more than some imperfectly self-replicating molecules to constitute a living organism.

Those molecules must also be able to somehow produce the required chemical products for self-preservation and replication. This alone should give one pause when considering the materialistic view of the origins of living organism.

Couple that with how this is done and any scenario requiring reducibility to matter, energy & time, is itself reduced to a fairy-tale, full of imaginary narratives and fanciful stories.

To further cement the design inference biology textbooks tell us of alternative gene splicing, (molecular) chaperones and transit peptides (also called signal peptides, signal sequence

Alternative gene splicing refers to the process in which mRNA is edited before it leaves the nucleus to rendezvous with the ribosome.

Genes are littered with sequences called exons and introns. Introns (almost) always get cut out from the mRNA sequence. The remaining exons can be left to form as they are or any number may be cut out thus changing the configuration of the mRNA product.

This is how one gene can code for multiple products. Which is why the “gene count” for any one organism may not be an accurate depiction of the number of proteins and other molecules coded for by the parent DNA. It also defies an explanation reducible to matter, energy & time. (nor reducible to parsley, sage, rosemary & thyme)

Chaperones- as one article has it:

Molecular chaperones have an essential role in the regulation of protein conformation states -- the process during which transient or stable interactions with client proteins affects their conformation and activity. Chaperones capture unfolded polypeptides, stabilize intermediates, and prevent misfolded species from accumulating in stressed cells.-- Roles of Molecular Chaperones

Another tells us:

It has recently become clear that protein folding in the cellular environment is not a spontaneous, energy-independent process akin to that observed when chemically denatured purified polypeptides are refolded in vitro. Rather, in vivo protein folding strongly relies on accessory proteins known as molecular chaperones and foldases.--Molecular Chaperones and Foldases

IOW it has become clear that protein folding is not reducible to matter, energy & time.

That article goes on to say:

Molecular chaperones are a class of proteins that have been highly conserved in all kingdoms of life and identified in most organisms and cellular compartments examined to date. They are defined as proteins that help other polypeptides reach a proper conformation or cellular location without becoming part of the final structure.

Transit (signal) peptides, (N or C)-terminal extensions- these are interesting little starting sequences and tails that direct the protein to its proper destination. And if there is a membrane in the way it holds the key that allows the protein through.

Once at the destination this sequence gets cut off and is not part of the mature protein.

So there you have it- the basis for design detection in living organisms.

Let the evotard hand-waving begin...