|Evolution of DNA -
Once the first Foxy genes became established and useful, it seems likely that cells would have started to use variations of the same gene in different places.
A digital 'script' is such a great way to specify cell structures, that over time it probably became the dominant way for eukaryotes to specify the structural details of their cells.
As with other genes during its period, the first Foxy would have been marked with an ID sequence, and probably was managed by some sort of regulatory process that would control its expression.
So once Foxy was doing something useful for the cell, natural selection would have worked in parallel on several different aspects of Foxy:
1 The script that Foxy read would evolve to whatever sequence created the most effective structure.
2. The proteins assembled into the structure would evolve to whatever worked best for that structure, and whatever was guided most effectively by Foxy.
3. The Foxy protein itself would evolve to work more effectively at RNA-reading and structural placement, and to be regulated more smoothly.
4. The regulatory system would move towards optimum timing and placement for the structure created by Foxy.
Investigating the impact of mutations on any given Foxy system is complicated, since there are several places where a mutation might have an impact. The complete system would probably involve multiple steps, and any of them could be affected by a genetic flaw. Here's a possible sequence for a typical structure specified by a Foxy:
A regulator protein takes a gene ID sequence, and uses it to locate a particular Foxy protein. It may also move the Foxy to a particular part of the cell where the structure should be located.
A mutation in the gene ID in step one would mean the wrong Foxy protein would be used to position the structure. If that Foxy is completely ineffective, the structure would not even be formed. If the wrong Foxy is only partly effective, then the structure might end up being distorted somehow.
A mutation in the correct Foxy gene would have a similar effect, though it might be much more lethal if the same Foxy protein is used to specify multiple structures.
A mutation in the gene ID in step two would mean that the cell would still build the structure from the usual components, but they would be arranged in a different order. That might mean a very distorted structure if the script was very different from the correct version.
A mutation in the proteins created in step three would be a usual protein mutation, no different from any 'regular' mutation.
Foxy Script Mutations
Mutations in a Foxy script would tend to have a different effect than similar mutations on one of the Foxy proteins or ID sequences-- the result would depend entirely on the nature of the Foxy script.
A small mutation in a low level script might have an extremely small phenotypic result. For example, a random mutation in a script positioning cilia on a cell might result in a single missing cilia, an extra cilia, or a cilia shifted out of position slightly. These are the kinds of changes that researchers probably view on a daily basis, and routinely write off as random environmental effects instead of genetic changes.
A mutation in a high level script controlling major cell functions might cause a very dramatic change. For a highly optimized major structure, any change in the script itself might be deleterious. That would mean that the script sequence in an intron would actually be more homogenous (genetically conserved) between individuals or species than the protein-coding exons surrounding it .
Foxy and Speciation
From an evolutionary point of view, the hard part is creating a new Foxy gene that does something that was never done before. Adding Foxy control to a new structure would be a rare event that might be equivalent to introducing an entirely new phylum of cells.
Once that happened, fairly normal evolutionary selection would result in script changes that would produce a variety of successful progeny-- equivalent to the introduction of new genera or species. That kind of change could take place in just a few generations, as scripts changed and eventually arrived at an optimum configuration for the new structure.
Or, in still other words, life may have come up with a reasonably perfect set of metabolic proteins during its first billion or two billion years of evolution. And in the past two billion years since then, nearly all of the evolutionary changes may have happened in the scripts that control them.
The evolutionary path of many organisms has been marked by occasional periods of rapid transformation, interspersed by long periods with little or no change.
The split between slow changes in Foxy proteins and fast changes in scripts fits in with that picture very well.
It's not easy for evolution to 'design' a new cell feature, and work out the kinks so it is actually beneficial for a cell. So that kind of improvement is relatively scarce in the evolutionary record.
Whenever a new Foxy-controlled structure does manage to emerge, there would be the period of rapid adjustment as organisms starting using it to improve their lives. They'd expand into new niches, and undergo other changes to support and enhance the new cell whatever. Meanwhile, surrounding organisms would also change relatively rapidly, because of the resulting changes in their own environment.
After that period of revolutionary change, cellular evolution would settle down to a period when each organism would stay about the same, with occasional 'tweaking' of scripts to reach an optimum state for some local niche.
Decoding Foxy Scripts
Nowadays it is easy to take a DNA sequence, and translate it into a sequence of amino acids in a protein. Scientists are even getting better at deducing the function of a newly discovered protein, based on its shape and active groups.
Unfortunately, decoding Foxy scripts is not so simple.
Different Foxy proteins would almost certainly use different methods to parse the data in a script, and we would need to know something about the function of the data, before being able to understand what it means.
The situation is not unlike modern computer data. Protein-coding DNA is akin to computer executable programs, which contain data that can be 'disassembled' to understand how the program works. Script DNA is akin to data files, which are useful when you open them with the correct program, but a mystery otherwise.
To understand the action of Foxy scripts, we'll need to identify each script (probably via its gene ID), link it to a specific script-based action, and then either observe the chemical process controlled by the script, or else view the results of various mutations, to see what impact they have on a cell.
What kinds of structures would have been most useful for early cells?
Well, the number one candidate would be to form even larger and better supercatalysts, for performing basic cell metabolism, and any new biochemical 'tricks' that might give the cell an advantage over its neighbors.
Way back in the days of Clem, we talked about the use of short helper chains that could link a few enzymes together, and make them more efficient. Then we talked about complementary pairing, and how it could do a better job of positioning enzymes and their raw materials.
The first cells that could use scripts to position proteins could have built really big enzyme complexes and structures, containing hundreds or thousands of proteins and helper molecules. Having that kind of enzymatic power, all in one place, might have accomplished something new and useful for the cells-- anything from photosynthesis, to more efficient production of cell raw materials, to production of useful new toxins to use for zapping enemies.
Besides allowing for macro-scale control, the scripts would have also 'digitized' the structural specs, making it easier for cells to drift into the optimum arrangement of enzymes, thanks to the natural 'tweaking' done by replication slippage. You might say that adding script control made enzyme complexes much more evolvable.
One other area where scripts would have been extremely useful, is in the positioning of contractile fibers.
Early cells with fibers that could convert energy into movement would have gained an instant selective advantage over their neighbors, if only by randomly mixing the cell contents and getting metabolic products close to each other faster than via diffusion. That makes it likely that contractile proteins such as actin would have evolved relatively quickly in early cells.
Once there were contractile fibers, placing them in the correct places would have resulted in more controlled, useful motion, giving those cells an even greater advantage over cells that could only twitch randomly.
A Foxy script would be ideal for positioning contractile fibers in whichever way had the most selective advantage.
For example, an evenly spaced grid of contractile fibers around the outside of a cell would allow it to pulse, so it would be easier to expel or ingest materials through pores in the cell membrane or cell wall. The right sequence of pulses might even move the cell through its surrounding medium.
Different cells would have different survival strategies, so each would have its own optimum layouts of contractile fiber (which could have been easily specified by a layer or two of Foxy-based regulation).
Contractile fibers positioned via a more complex Foxy script would be a quick way for cells to develop useful eukaryotic cell functions like phagocytosis, contractile vacuoles, amoeboid motion and so on.
Contractile fibers are also important in cell division. In modern cells they pull the cell membrane or cell wall into the center to split the cell, and also pull the genetic material into each daughter cell so they each get a full complement of genes.
This function is so vitally important that it is a good candidate for one of the earliest places for the use of a Foxy script.
Cells that are capable of stirring their environment have enormous potential for increased survival value. It lets them move through their environment (especially if the cilial motion is coordinated), and also helps them to gather up food.
To get functional cilia, cells would have needed to organize proteins into a hair-like protrusion, and also connect it with contractile fibers. Doing that didn't require any chemical innovations, just the proper placement of existing materials-- so it's an ideal place where Foxy would have sped the pace of evolution.
Once a cell contained cilia, using Foxy would made it easier for cells to evolve into the optimum placement around the cell's exterior, and develop a system to coordinate their movement.
The flagella in bacteria and eukaryotes has been used as an example of 'irreducible complexity'-- meaning that it's a structure so complex that it is difficult to explain a development pathway, via Darwinian selection based on benefits at each step.
Some scientists have proposed a step-by-step evolution of flagella from secretory pores and other cell structures, but it still difficult to postulate the efficient positioning of each flagellar component via purely protein-based systems.
Other the other hand, once placement of pores, contractile fibers and other elements were under Foxy control, a simple script mutation might have placed several key components into the same place, via a simple script change. That would be a way for cells to create a working flagella much more rapidly than would otherwise be possible.
One cellular feature that is found in Eukaryotes but not Prokaryotes is phagocytosis-- the ability of a cell to engulf outside particles and bring them inside the cell for further digestion.
Once cellular contractile fibers were under Foxy control, the right script mutation could have produced an arrangement of fibers that would allow phagocytosis to occur.
Of course, being able to eat the neighbors would have given any eukaryote an enormous selective advantage.
To do a truly superior job of engulfment, cells could have used sensors as well, so they could notice whatever tasty morsels were worth popping into a food vacuole. Placing of sensor proteins and connecting them chemically to active elements would be yet another type of cell structure that would be perfect for Foxy to manage.
Photosynthesis requires a complex arrangement of proteins, pigments and coenzymes to transfer energy from photons to sugars.
Cyanobacteria probably evolved the ability to fully photosynthesize about 3 billion years ago, and it's quite possible that they did that with the help of some early Foxy scripts.
The chlorophyll and other compounds in Eukaryotic chloroplasts are much more highly organized than the similar compounds in cyanobacteria, and it seems reasonable to guess that this lumen structure is also controlled by a Foxy script.
As with mitochondria, some of the chloroplast proteins are also transcribed from nuclear DNA in the parent cell, so there is no clear evidence whether any scripts would be located in the chloroplast DNA or in the main cellular DNA.
So far we've talked about most aspects of scripts, but we still need to take a look at their impact on the DNA itself. Where is the best place for cells to store Foxy scripts?
Foxy and Introns
If the script is small, the best place to store a Foxy script is probably in an intron. That way the positioning data is conveniently close to the gene coding for the Foxy protein.
When the cell is ready to run a Foxy script, it would first made an RNA copy of the entire DNA gene (messenger RNA), including both the protein coding parts of the gene (exons) and any other materials (introns). The intron would pop out of the mRNA during the transcription process, and deliver the Foxy script to the Foxy protein that was just created from the protein-coding portion of the gene. It seems likely that the script would be located near the very end of the gene, so it could be delivered right when the Foxy protein was complete.
In other words, a Foxy script was about the same as any of the helper chains that cells were already using, and introns would deliver it about the same as always.
Some scripts were probably very long-- repeat this for the entire perimeter of a cell. That means that they may have been thousands or tens of thousands of nucleotides in length.
Adding such a long piece of DNA to the intron portion of a gene was probably not such a good idea. The problem is that each intron separates the exons (the protein-coding portions of the gene), and as the protein-coding portions of the gene grow further apart, there's an increasing risk that they'll be separated by crossing over or other genetic accidents.
Fortunately, thanks to gene ID, cells really could access a script from anywhere on the genome. Introns were close and convenient, and it was certainly simpler to store the data right next to the protein that used it. But if that caused problems in a cluster of genes, cells that could store the data in a different part of the chromosome would have had a significant advantage.
Once a Foxy found a way to retrieve its script from outside the main gene, it would have been the first instance of satellite DNA-- repetitive base pairs that are outside any protein-coding gene.
Of course, Foxy needed a good way to fetch and retrieve the script. To help with that, it's time to introduce another shifter of genes. This one is moderately similar to introns, and it can provide a solution to this problem.