Second draft of the RNA World Script

Here I have an updated version of the RNA world script. It flows better than the last one and is easier for new people to follow:

WHAT IS THE RNA WORLD HYPOTHESIS?

If you were to go back in time 120 million years, you’d find yourself in a Dinosaur World 500 million years ago was a world of trilobites and other strange sea creatures 3.4 billion years ago was the world of the first living cells And before that, scientists suspect that chains of a chemical called RNA, or something similar to RNA, kickstarted this entire beautiful mess we call life. RNA is thought to have given rise to life for several reason: chains of RNA are found abundantly in all living cells today, they’re close chemical cousins to DNA, and with very little help from researchers, RNA chains can replicate, evolve, and interact with their environments. While many details have yet to be worked out, the RNA world hypothesis is the simple idea that somewhere on our early planet, perhaps in a tide pool or hot spring, the Earth’s chemistry was producing random chains of RNA. Once formed, they began replicating, evolving, and competing with each other for survival. As these chains evolved and diversified, some eventually began cooperating to produce the genetic code, a wide array of complex proteins, and even living cells which from the perspective of RNA can actually be thought of as houses or “survival machines” for RNA to live inside. To understand how RNA chains can interact with their environments, replicate, and evolve; we first need to understand the simple process of base pairing. Chains of RNA are made of nucleotides — small molecules that come in 4 different types labeled A,C,U and G. The backbone atoms of a nucleotide (shown here as a yellow bar) can form strong chemical bonds with the backbone atoms of any other RNA nucleotide. This means that different chains can have completely different sequences from left to right. The parts we call the bases of nucleotides (the colored sections labeled A, C, U, or G) are attracted to other bases, sort of like a magnet, but they’re selective about who they will stick to: G selectively pairs with C, A selectively pairs with U. When bases find their matches and stick together, we call it base pairing. Researchers have found that with a little assistance, base pairing allows chains of RNA to replicate and evolve. Here’s how it works: When a long chain of RNA is suspended in cool water with high concentrations of free nucleotides, the chain can act as a template for its own replication. Nucleotides automatically base pair with their partners on the existing chain. If their backbone atoms form chemical bonds with each other (by the way, this part currently requires assistance from researchers) a complementary RNA strand is born—one with the exact inverse sequence of the original. If the water is then heated, paired bases release their grip, freeing both chains to act as templates when the cycle repeats. The great thing about this process is that every other RNA chain produced, is a copy of the original but sometimes mutations slip in. This means that as chains compete for survival and reproduction, true evolution - descent with modification, acted upon by selection - can operate on chains of RNA. As amazing as replication is, base pairing also gives RNA chains a second special ability. When placed in water cool enough for base pairing but without enough free nucleotides for replication, chains will fold up and base pair with themselves. The end result is a complex shape with certain sticky bases pointing outward because they weren’t able to find partners. These sticky outward facing bases can cause unique chemical reactions, by interacting with other molecules in their environment. A folded chain of RNA capable of guiding a specific chemical reaction is what we call a ribozyme. Some ribozymes break certain molecules apart, others join certain molecules together. A ribozyme’s specific function is determined by its specific shape, and its shape is determined by its sequence. If a mutation changes a ribozyme’s sequence, the shape can be modified and so can its function. When ribozymes were first discovered scientists wondered how difficult it would be for random chains of RNA to evolve legitimate survival functions. Imagine, for example, a ribozyme that could build nucleotides out of molecules it finds in its environment. Across multiple generations, natural selection could promote and refine this ribozyme because the chain would tend to have access to more free nucleotides than its rivals, allowing it to replicate more often. Motivated by curiosity, researchers at Simon Fraser University produced a large group of random RNA chains, and examined them to see if any happened to be able to make nucleotides. Surprisingly, some actually could, but they weren’t very efficient. Researchers selected out the successful chains and then used a lab technique called PCR to quickly replicate them with slight random mutations. After just 10 rounds of PCR followed by selection, highly efficient ribozymes evolved — these are molecules with the life-like ability to actively participate in their own survival! These ribozymes, and many others produced through similar experiments, are beginning to blur the line between living things and simple chemistry. So to sum things up, the RNA world hypothesis is the simple idea that the first things to replicate and evolve on our planet may have been chains of RNA, or something similar to them. While the basic idea of the RNA world does seem to give us a promising pathway to the origin of life, it’s still a work in progress. As mentioned, one of several unsolved problems is how did nature get backbone binding to function without the special enzymes or the lab techniques we use today? While many researchers continue to focus on RNA, others are investigating alternative molecules — chemical systems that might replicate and evolve without assistance, and could have given rise to RNA. Continual breakthroughs are being found in both avenues of research.

False Claim in Evolution 2.0 - All codes whose origin we know are designed

This is the fourth post in a series reviewing Perry Marshall's Book Evolution 2.0, Breaking the Deadlock Between Darwin and Design. To see the first post with links to each article in the series, start here. 

In Perry Marshall's book Evolution 2.0, he falsely claims:

"All codes are created by a conscious mind; there is no natural process known to science that creates coded information. Therefore DNA was designed by a mind." (pg 192, emphasis added)

On his website he gives us a challenge, offering millions of dollars to the person that can prove him wrong (though, as you'll see in my post on the challenge, it's specifically worded so that he will never have to pay). In the challenge he says:

"Show an example of information that doesn’t come from a mind. All you need is one" (pulled from cosmicfingerprints.com/solve/ on June 3, 2016)

In his book he goes on to say:

"The prize goes to the first person who discovers a natural process that produces a complete communication system without having to specify (design) the encoding and decoding rules in advance. Such a process, if discovered, would revolutionize modern science." (pg 201, emphasis added)

Well, as it turns out, scientists have discovered a natural process that produces code without a mind, and it did revolutionize modern science! It's called... wait for it... evolution by natural selection!

In my last post I showed how creatures with minds can develop "communication systems without having to specify the encoding and decoding rules in advance". If you haven't yet read that post, I recommend doing so before moving on. Here I will build on that post showing how the same simple rules can allow any two evolving entities, with or without thinking minds, to develop communication systems as well. Intelligent designers need not apply.

Here we'll look at not just one, but two of the many known and documented examples of evolved communication systems: that between plants and pollinators, and that between bacteria. After each example I'll outline what we know about how each system evolved. Finally, I'll end by showing how Perry Marshall could edit his book to make it accurate.

Evolved Communication System Between Plants and Pollinators
Flowering plants, even though they don't have thinking minds, actively communicate with insects and other pollinators on a regular basis. This communication system evolved under selective pressure to improve their reproduction. Insects carry plant pollen (similar to sperm in mammals) from one plant to the next, where it's able to fertilize the second plant's seeds. In simple terms, bugs help flowering plants have sex. Flowers are relatively new in evolutionary history, the first fossils date to about 130 million years ago. Most plants before then used wind or environmental water to transfer their sperm to other plants instead. Insects, however, are much more efficient.

Flowers act as encoded messages between plants and pollinators. Bright colored pigments and strong smelling fragrances are signals, telling animals that the plants are ready for pollination. A nectar treat is often provided as a bribe to get the animal to do the work (though some insects simply eat pollen, spreading crumbs from plant to plant which also does the job). When a flower has been thoroughly pollinated, the plant stops producing fragrances, and produces oxidizing enzymes instead. These enzymes dull the pigments and eventually kill the petals of the flower. A simplified breakdown of the plant's evolved code can be understood as follows:

The plant encodes the message, transmits it via the flower, and the bee (or other pollinator) decodes the message and obeys its orders. This is a legitimate coded system that developed without any need of intervention from a designer.

How did the flower communication system evolve? 
In the last post we learned that in humans and other thinking animals, codes can emerge from noise through a process described in signalling theory:

1. Cues are accidentally transmitted by a sender
2. Meaning is assigned to the cue by a receiver
3. The sender, if rewarded for sending the cue, can then amplify the cue, making it a "signal"

This process works quickly for creatures with brains, but also works on a longer time scale for anything capable of evolving through descent with modification, acted upon by selection.

The evolution of flowers

While we can't go back in time to see how flowers initially evolved, we can examine fossil evidence, as well as look at examples of non-flowering plants alive today for clues on how this ability may have evolved. To keep things short, I'll just go over comparative anatomy here.

Before flowers evolved, plants mainly transferred pollen to their mates via the wind or moving water. Many of these plants' descendants are still alive today and continue to use the wind. A cone from Pinus taeda is shown below. When the season is right, it releases puffs of pollen into the air to be carried by the wind to potential mates.

By Pinethicket at English Wikipedia

Pollen is extremely nutritious and is, therefore, eaten by many insects. As you can see above, the bright yellow pollen can act as a visual cue, accidentally alerting insects of its presence. This is step 1 in the process of evolving a signal!

Any insect that either learns or evolves to associate the color yellow with pollen, will have access to nutritious food and be favored by natural selection. This is step 2 in the process of evolving a signal!

Many plants defend against pollen eaters by producing bad tasting or even toxic chemicals in their pollen. Other's, however, have evolved to exploit the pest's activities. Pollen eaters often visit multiple plants in their quest for food. Any pollen stuck to their bodies can pollinate female cones on other plants. This can give a plant a reproductive advantage because insects are often more accurate than the wind at finding the other cones that need to be fertilized. Under these conditions, any mutation in a plant that makes its pollen cue stronger (brighter colored pigments for example) can be magnified by natural selection. Once this happens, Step 3 in the development of language has occurred, a legitimate signal has evolved!

Beetle attracting pollen cone - Photo by L. Shyamal 

There are several examples of non-flowering plants that have evolved signalling behavior with insects. In many cases, it's much milder than what we see in flowering plants. Cycadales for example, are an order of gymnosperms (non-flowering plants) that have developed a pollination relationship with beetles. Pigmented cones appear to act as a signal to the beetles when pollen is ready. Smilar signaling strategies have evolve in other species. Studying these systems helps us understand how the flowering system likely started.

Evolved Communication System Between Bacteria
Bacteria are tiny creatures living in a world of giants. As such, it's often a survival advantage for them to work as a group to get a task done, either when digesting a large food source, or trying to defend against an enemy. Bacteria don't have eyes, ears, or thinking minds like we do. That said, they have evolved communication systems that allow them to detect and then automatically coordinate their efforts with neighbors.

Many bacteria make and send out chemical signals called acylhomoserine lactones (AHLs)  which you can think of as smells. Most species studied have at least one scent or “word” they use to communicate with others of their kind. The system consists of an enzyme (encoder) that produces the communication molecule (message) which then seeps out into their surroundings. A receptor on the cell wall (decoder), which is similar to the receptors you have in your nose, detects the scent and triggers the bacteria to behave in a specific way.

When a bacteria is alone, it will catch an occasional whiff of its own AHLs but the scent is weak. When the bacteria is surrounded by friends, the smell is overwhelming, triggering behaviors that are only successful when all the cells participate in unison.

This is how bacteria of the same species talk and automatically coordinate their efforts.

For the most part, each species has it’s own AHL molecule which can only be detected by other members of the species. This essentially means their language consists of one word, and is private. That said, most bacteria also make a universal molecule called AI-2.

At least two species, Vibrio harveyi and Salmonella typhimurium, have receptors for their own secret AHLs, but also have receptors that detect AI-2s from other species! This means that in their world, not only can they smell how many friends are near, they can also smell how many strangers are around. As you might expect, different behaviors are triggered by different ratios of AHLs and AI-2s.

Many more signals in the bacteria’s language likely exist and are just waiting for us to discover them. That said, we can present what we know so far in the translation chart below:

How did bacterial communication evolve?
So far, the origin of the AHL molecule has not yet been discovered. AI-2, on the other hand, is now known to have started out as.... wait for it... an accidental cue!

Researchers initially thought AI-2 was a special molecule produced exclusively for inter-species communication, but in 2002, AI-2 was discovered to be a simple waste product, bacterial urine if you will.

Vibrio harveyi and Salmonella typhimurium both evolved receptors to pick up on the cue which essentially allows them to count strangers. Both have since evolved unique behaviors that are triggered by the smell of strangers, and it appears they have also evolved ways to control when and how much AI-2 they will release. If it's true that they really can control release of AI-2, then it has gone from being a simple cue, to a legitimate signal!

How Perry Marshall's book should be edited

Biologists have been studying and carefully documenting the evolution of coded communication for several decades now. If Perry wishes to be honest in his portrayal of scientific knowledge, the message of his book should be modified as follows:

"DNA is code. All codes whose origin we know are either designed by a mind, or have evolved through natural selection. Therefore, the genetic code was either designed by a mind, evolved, or produced by a currently unknown process."

Most scientists investigating the origin of life are doing so under the hypothesis that the genetic code evolved into its current form. This hypothesis brings us to the question of our next post: Can evolution work without the genetic code?

Spoiler alert, the answer is yes!

Further reading
Signalling theory and the use of language in bacteria
Flowers and the fossil record New cue detection directly observed evolving in bacteria (in this case, they detected a new food: D-Arabinose) An overview of signalling theory with many examples of naturally evolved communication systems (see chapter 14)

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