Did whales evolve too fast? A look at the claims of Richard Sternberg

Summary: Creationist and biologist Richard Sternberg claims that the evolution from Pakicetid whales to Basilosuarid whales (Dorudon and Basilosaurus) happened too fast for natural processes to have caused the changes. To support his conclusion he lists 15 changes that he claims had to occur in the 8-10 million year gap between the two groups of whales. Here I have fact checked each of his 15 claims. I found 4 to be true, 2 to be partially true, 5 to be invalid, and 4 to be false. I give explanations for how I rated each claim, with links to the real evidence for you to see for yourself.

Science is the collection and documentation of observable facts, and an ongoing discussion about how those facts can be best linked together. Though Sternberg is trained in science and may be capable of doing good work elsewhere, in this instance he failed to make a legitimate scientific case for his conclusion.

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One of the earliest fossil creatures accepted as a link to modern whales is Pakicetus attoki, bones of which date back to between 58 and 42 million year ago. The species had 4 legs and certainly walked on land but also has abnormally heavy bones and eyes placed high on skull, both of which are trademarks of aquatic or semi-aquatic hunters. Tooth chemistry studies tells us that Pakicetus was likely a freshwater hunter.

Unfortunately, a full individual skeleton of Pakicetus has never been found, leaving us to reconstruct this animal with bits and pieces. That said, fragments of many different individuals have been found, allowing us to construct a near full skeleton of the animal.

8 to 10 million years later, we find Dorudon atrox, a fully aquatic whale with tiny hind legs (modern whales no longer have hind legs), hands that form flippers (similar to modern whales), and tail bones that strongly suggest it sported a tail fluke similar to modern whales. It lived and hunted in saltwater. We have several extremely well preserved specimens of Dorudon (and its close relative, Basilosaurus) in the fossil record, making it a wonderful species to glean information about whale evolution.

In-between the two groups we find a rich fossil record of diverse whale-like species, unfortunately, most are known only from partial skulls.

It's largely assumed, because we don't yet have any earlier fossils than Pakicetus confirmed (though some are suspected), that a transition between these two forms (Pakicetus and Dorudon) happened in a relatively linear pathway during that 8 million year time span separating the two groups.

Several years back, Richard Sternberg made a speech that has become popular among the anti-evo community. In it, he claims that 8 million years isn't enough time for that transition to have taken place because there are too many changes that occur between the two groups. In his speech he lists 15 changes. Because Sternberg is a trained scientist and geneticist, I feel it's worth considering his claims.

Above is his speech for you to hear for yourself. Below, I have outlined the 15 changes he said must have happened during that 8 million year transition. I have fact checked them to see if they are indeed valid. I have rated each claim as either "True", "Partially True", "Invalid", or "False". These are my results:

Claim 1 - They would have had to evolve a countercurrent heat exchange system because testes moved from outside to inside the body

False: All mammals already have a well developed countercurrent heat exchange system which we use to cool off body-parts that are too warm, including... wait for it... our testes! When you blush while running, you are using this countercurrent heat exchange system too cool off internal organs. If you're a guy, you may have noticed a change in blood flow to your testicles as well after a run. Yep, that's the countercurrent heat exchange system doing its thing. To learn more about it, read this articles about bull testes: http://extension.missouri.edu/publications/DisplayPrinterFriendlyPub.aspx?P=G2016

Furthermore, even if this first claim wasn’t false, it would be invalid because we don’t know what pakecitid testes or basilosaurid testes were like. Testes didn’t fossilize in either group. It’s possible both had external testes but it's much more likely they both had internal testes. Why? Because hippos, the closest living relatives to whales, have internal testes and likely inherited them from a common ancestor with whales before Pakicetus. For more on hippo testes, here’s a fun read.

Claim 2 - They must have evolved ball vertebra because unlike a dog’s tail that wags side to side, whales need a tail that moves up and down
Partially true: Apparently Richard Sternberg he has never seen a dog up close before. They can move their tails up and down as well as left to right. Maybe he's talking about what are called ball vertebra at the end of the tail where the fluke is in Basilosaurids. These are small, rounded tail bones without projections, allowing for more flexibility of the fluke. Pakicetus is not known to have ball vertebra at the end of its tail.

This means there needed to be a reduction of projections in the tail bone. Reductions are pretty easy for evolution to do. Many dog breeds, for example, have reduced tail bone numbers.

Claim 3 - They need to have evolved tail flukes
True: Basilosaurids have clear signs of tail fluke attachment on the end of the tail, pakicetids do not. That said, while bones can’t tell us for sure, pakicetids may have had flattened tails like otters.

The transition from a land mammal tail to a fluked tail is not shown in the fossil record because flukes, being made mostly of cartilage, don’t often fossilize. That said, we can easily think of a gradual step by step process starting with a widening of the tail, then a gradual migration of that widening to the end of the tail. For real modern examples of several possible steps in this transition, see an otter tail, then a beaver tail, than a manatee, then a dugong. Could this have been a the way flukes evolved? With the data currently available, we cannot yet be certain.

Claim 4 - They had to evolve new musculature for the tail fluke
False: Tail flukes don't have muscles, they are cartilage structures. Muscles of a whale tail are larger than those found in most mammal tails but they appear to be the same muscle systems (the epaxial mass and hypaxial mass) that normal mammal tails have. http://www.whalesforever.com/whales-fins-and-flukes.html

Claim 5 - They need need to have reorganization of the kidneys to drink salt water
Partially true: Tooth chemistry in pakicetids strongly suggests they were mostly freshwater animals and basilosaurids were mostly salt water animals. That said, kidney changes between freshwater mammals and saltwater mammals are small. No need to reorganization. The only change needed is the elongation of internal structures called “loops of Henle”. Here’s a video on the loop of henle: https://www.youtube.com/watch?v=cYyJF_aSC6o

The loop of henle varies in length from individual to individual which is one of many reasons we vary in how much salt and alcohol we can safely consume. Natural selection simply need promote one length over the other to adjust a species to a new environment.

Here’s an article about the anatomical difference between saltwater mammal kidneys and freshwater mammal kidneys: http://www.scientificamerican.com/article/how-can-sea-mammals-drink/

Interestingly, according to tooth chemistry analysis, Ambulocetus—a species representing a transitional branch between pakicetids and basilosaurids—lived in brackish water. This is the perfect way to transition from a freshwater to a saltwater environment.

Claim 6 - They have to evolve the ability to nurse underwater

Invalid: Yes, whales nurse underwater but so can hippos, their closest living relatives (they also nurse on land sometimes). This means the trait likely arose before the lineages split and that pakicetus was already nursing underwater. The claim is completely irrelevant to the 8 million year gap between pakicetids and basilosaurids. Here’s an article about hippos nursing both on land and underwater. http://blogs.sandiegozoo.org/2011/02/02/baby-hippo/

Claim 7 - The nipples had to be modified for underwater nursing

False: From the mother's perspective, nursing works exactly the same in the water as it does on land. In whales, as is the case for most mammals with long snouts, the calf sticks out and curls it's tongue around the nipple, creating a straw for them to drink through. As mentioned, hippos nurse on land and underwater with no problems.

In modern whales, nipples are tucked under flaps of fat in the skin but that’s for the mother to swim without drag, not to aid in suckling. We don’t know if the fat flaps were present in pakicetids or basilosaurids so even that fat flap is invalid to Sternberg's argument.

Claim 8 Orientation of fetus has to change

Invalid: This claim is invalid because we don't know how pakicetid or basilosaurid babies were carried in the womb.

I assume he basses this claim on a specimen of Maiacetus (a genus of whale between pakicetids and basilosaurids) that has a fetus in it's abdomen with it's face pointing toward the mothers hind quarters. This suggest it would have been born head-first. This is in contrast to most modern whales that give birth tail first. That said, the orientation of the fetus in Maiacetus may not have been how it would have been during birth since fetuses often switch orientation multiple times during pregnancy. Furthermore, hippos (the whale's closet living relatives) usually give birth hind-first just like whales, and often give birth in the water. This means the adaptation of hind-first birth in whales may well have occurred before pakicetus.  Here’s a film of a hippo giving birth in the water: https://youtu.be/pGxi-ZNMsaU

Here’s film of a hippo giving birth on land showing they have babies hind-first: https://www.youtube.com/watch?v=oLieIaWWDbQ

Claim 9 - The hind limbs must be reduced

True: Pakicetids have long hind legs, basilosaurids have super short hind legs. This is the biggest change that we know occurred between the two groups of whales.

Claim 10 - Forelimbs transform into flippers

True: That said, this is not a difficult transition for evolution to make. In fetuses, the hands of all mammals start out as flippers, then, between the finger bones, a process called apoptosis (cell death) begins to “cut” the space between fingers. To give webbed or flippered hands, this process can start late, end early, or not occur at all. Many different types of mutations can cause apoptosis to slow down, speed up, or fail, resulting in flippers or webbed hands. https://en.wikipedia.org/wiki/Apoptosis. 

Claim 11 - They needed to evolve new hydrodynamic properties of the skin

Invalid: It is true that a modern whale's skin is way better than ours at resisting degradation in water, that said, whales didn't evolve from humans, they evolved from artiodactyls. Modern artiodactyls (such as hippos) have wonderfully waterproof skin. This adaptation was likely already present in pakicetids. As mentioned, many features of pakicetid skeletons suggest they were living a largely aquatic lifestyle. Here's an article about their aquatic features: http://link.springer.com/article/10.1007/s12052-009-0135-2

Claim 12 - They need special lungs

Invalid: we don’t know what pakicetid lungs or basilosaurid lungs were like so this issue is not actually relevant to his argument. Modern whales lungs aren’t much different from normal mammal lungs but they are more efficient. These efficiencies might have evolved before pakicetids, between pakicetids and basilosaurids, or after basilosaurids but before modern whales. There is no way to tell from the fossil record. 

Claim 13 - Whales had to evolve novel muscle systems for the blowhole 

False: First off, mammals already have muscles to power their nostrils, even humans (though ours are super small). Here’s video of hippos using their nostril muscles in a way almost identical to how baleen whales use theirs: https://www.youtube.com/watch?v=86ZHdF9hmig

Toothed whales (dolphins and the like) seem, at fist glance, to have novel muscles in the melon and blowhole but it has not been confirmed that these muscles are actual new. Instead, while more studies need to be done to know for sure, it appears that in toothed whales, the muscles of the lips have migrated up into the head for use around the melon and inside the blowhole. This appears to be the case when we watch the face structures develop in dolphin fetuses and when we note the lack of lip muscles in modern toothed whales. Notice how these dolphins no longer have movable lips like hippos and other mammals: https://www.youtube.com/watch?v=KMZ7oOCXfP8

Furthermore we don't know what the muscles in pakicetid nostils or basilosaurid nostrils were like, making Sternberg's claim invalid on-top of being false.

Claim 14 - The eyes must be modified

Invalid: Again, we don’t know what pakicetid eyes were like nor do we know what basilosaurid eyes were like. We have no way of knowing if any significant changes occurred in eyes between the two groups.

Claim 15 - Modification of the teeth had to occur

True but not significant: The teeth of pakicetids and basilosaurids are similar but basilosaurids are simpler (missing one cusp on the molars) and rougher (have a jagged top). Teeth can be compared in skulls here: http://link.springer.com/article/10.1007/s12052-009-0135-2

CONCLUSION

Only 4 out of 15 of Sternberg's "facts" were actually true. His conclusion that there was not enough time for whales to evolve is not verified by the data he puts forth. 

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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False claim from Evolution 2.0 - The rules of a language are always defined in advance

This is the third 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. 

On page 185 of Perry Marshall’s book, Evolution 2.0, we see 1 of 3 major factual errors the author makes throughout its pages. Don’t get me wrong, the book contains many more than 3 factual errors but this one is the first of 3 that erroneously lead him to his big conclusion: the genetic code must have been intelligently designed.

“The rules of any communication system are always defined in advance by a process of deliberate choices. There must be prearranged agreement between sender and receiver, otherwise communication is impossible.” page 185, emphasis added

This claim is presented time and again throughout the book as what he thinks is an impassable chicken-and-egg conundrum. Each time he insists the rules of a code or language must be designed in advance. 

“The broader question of life itself is a chicken-and-egg one... why would a code appear before there was anything to code?” page 202, emphasis added

While it is true that some codes/languages have been designed in advance (binary code, morse code and so on), this is actually the exception to the norm. Languages usually emerge gradually from accidental ques. Here I’ll show you how intelligent creatures (like humans, dogs, and birds) are able to use their brains to develop languages from ques. In future posts I’ll show you that creatures without thinking brains, and even what most people would consider to be non-living chemical systems, are also capable of developing codes from accidental cues through the simple process of evolution—descent with modification, acted upon by selection.

The entertaining case of an emerging new language between humans

I have an identical twin brother. His name is Mike. When we were born our parents spent many hours each day playing with us and speaking to us in hopes that we might learn English—a communication system with rules established well in advance, just like Perry Marshall would expect. The problem was, no matter how much time my parents spent with us, Mike and I spent even more time with each other.

Though we were slowly learning English, at about 2 years old we had also established a mini-language of our own that our parents didn’t understand. Simple as it was, we used it successfully to coordinate secret plans like how to steal candy our parents had stashed on top of the refrigerator, or how to unravel and flush entire rolls of toilet paper without getting stopped by our Mom. Sadly, the only word from our secret language that I still remember today is “guguk”. It means “candy”. How did this word develop?

If we were to take Perry Marshall’s claim literally—that “the rules of any communication system are always defined in advance”—we would be forced to assume that some outside intelligence, God perhaps, delivered the word “guguk” into our minds with the meaning defined in advance. This, however, is clearly not true.

According to people who study signalling theory, when both the sender and receiver have assigned meaning to a word (or a behavior, smell, sign ect), researchers call the word a “signal”. When only the receiver has assigned meaning to a word, researchers call the word a “cue”.

To see how this works for things beside words, let’s leave the babies for a second and think about bears in the woods.

An aside about bears, signalling theory, and the Boy Scouts of America!
Humans and bears have clashed violently for centuries. Black bears can usually overpower humans in a fair fight but it’s risky business and humans usually cheat. Because of this, bears don’t usually like to take their chances. If loud enough, the sounds that humans accidentally make with their feet when walking through the woods act as “cues” for the bears, alerting them to our presence and allowing them to run away long before they find themselves in fighting distance. In this case, the accidental sounds we make are considered “cues” by researchers, because at this point, only the bear (the receiver) has assigned meaning to the sound.

Because bears sometimes don’t hear footsteps until it's too late, as a Boy Scout, I was told that when walking through dense bear territory, I should stomp my feet extra hard or loudly sing. This would make sure any bears knew I was coming and allow them to distance themselves before an encounter. When behaving like this, researchers would say that I went from sending an accidental “cue”, to actively sending a “signal” to the bear.

When senders of cues are rewarded for transmission and begin magnifying their cues, the cues officially become signals.

Now back to the story of my brother and I:

The word “guguk” didn’t start out as a signal. Like footsteps in the forest, it started out as an accidental cue. Babies like to babble and the sounds of their babbles often change with their moods. One of us (we don’t remember which one but let’s just say it was Mike) tended to babble in a similar way every time he was eating or seeing candy. He was accidentally transmitting a cue. I noticed this cue and made an association. Each time I heard the transmission, I knew to look his way and I would likely find sweets. Maybe the sweets were being handed out for free, or maybe Mike spotted them in some hiding place. Either way it was worth my attention.

Once Mike realized I regularly responded to his accidental babble of “guguk”, he started magnifying the babble, making it louder and clearer to alert me of candy. He might have done this out of goodwill (we are close friends and, like many social animals, we are rewarded with pleasure from helping each other out). Mike might have also been alerting me to the presence of candy for more selfish reasons—he wanted my help getting it. In either case, the act of him magnifying the cue to modify my behavior transformed the noise from an accidental cue, to a meaningful signal. A legitimate language was beginning to emerge.

3 simple steps for producing language from accidental cues

In a simple 3 step process, Mike and I had transformed noise into language

1. Cues are accidentally transmitted by a sender (in this case, Mike's babbling)
2. Meaning is assigned to the cue by a receiver (in this case I associated the babble with candy)
3. The sender, being rewarded for sending the cue, amplifies the cue, making it a signal (in this case, Mike pronounced the babble "guguk" louder and clearer in hopes that I would respond)

Humans are instinctively obsessed with verbal language. We constantly mimic and deliberately try to learn and teach the meanings of signals to each other. These behaviors speed up the process of code production but these special human traits are not actually needed to get the process going. Any two entities that are either capable of learning with their minds, or adapting to their surroundings through the process of evolution, can develop codes for communication through this simple 3 step process.

Contrary to Perry Marshall’s repeated claim in his book Evolution 2.0, languages/codes do not need to be decided upon in advance. Languages can emerge as two learning or evolving entities interact with and adapt to one another.

The unpassable chicken-and-egg conundrum Perry Marshall thinks he has found is simply an illusion. In the next post I’ll show how languages emerge between evolving entities that don’t have thinking minds.

Further Reading

For more information on how languages emerge, there are many places to learn about signalling theory. It has developed in many different fields and has wide applications. Below are two of my favorite overviews:

Overview of Signalling theory in business

Overview of Signalling theory in biology

This is the third 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. 

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What is the RNA world hypothesis?

This is a draft script for my upcoming animation on the RNA world. Please comment below, I will read and consider your ideas for improvement. By the way, this is intended to be a voice-over with animation. I promise it will be way easier to follow once moving graphics accompany the text :) All living creatures today (even viruses which some people don’t consider to be alive) reproduce and evolve using a gene-protein cycle. If we look at a cell for example, information encoded in its genes is used to produce functional proteins called enzymes. Some of those protein enzymes then turn around to make copies of the cell's genes, allowing it to reproduce. 

An enzyme, by the way, is a molecule capable of directing specific chemical reactions. Different enzymes do different things. One might specialize in breaking down sugar for example, another might construct the building blocks of the cell wall. An enzyme's distinct function is determined by its 3 dimensional shape and its polar charge.

Because the gene protein system forms a closed loop, it presents us with a classic chicken or egg conundrum: Which came first, genes or the protein enzymes that genes code for? 

While the details are still not fully worked out, a series of discoveries over the past few decades have lead researchers to a surprising possible solution: What really came first? Genes that ARE enzymes. 

When the study of genetics kicked off big in the 1950s, it was initially assumed that genes could only do one thing: carry information about how cells should build proteins. Information carrying genes could be made out of DNA, or it’s close chemical cousin, RNA. 

In the early 1980s, research teams lead by two scientists, Sidney Altman and Thomas Cech, independently discovered stretches of RNA that were not carrying information about how to build proteins. Instead, when conditions were right, the RNA chains would fold into complex 3 dimensional shapes, becoming functional enzymes themselves! No protein needed! 

Because these enzymes are made of RNA (ribonucleic acid) today we call them ribozymes.

The RNA world hypothesis is the idea that before the genetic code and the gene/protein cycle ever existed, RNA chains were forming naturally. Once formed, some of these strands happened to be able to function as ribozymes, and were even able to evolve by making copies of themselves with slight accidental variations.  

To understand how RNA chains could capable of replication and evolution, and to see how they can fold in on themselves to form ribozymes, we first need to understand how base pairing works.

An RNA chain is made of nucleotides, small molecules that come in 4 different types labeled A,C,U and G. 

The backbone of a nucleotide (shown here in yellow) can form a really strong bond with the backbone of any other nucleotide. This means the letter sequence of a chain from left to right can be random. Different RNA chains can have completely different sequences. The part we call the base of a nucleotide (the colored parts labeled either A, C, U, or G) are attracted to other bases, sort of like magnets, but they’re selective about who they want to stick to: As only stick to Us, Cs only stick to Gs.

When basses find their matches and stick together, we call it base pairing. 

When an RNA chain is suspended in water with drifting nucleotides, the chain acts as a template for its own replication. Drifters will base pair with their partners on the parent chain and if the backbones of the newly attached nucleotides are then permitted to bind (which, by the way, easier said than done), a complementary RNA strand is born, one with the the exact opposite sequence of the parent chain. Temperature changes in the water can cause the two chains can separate, both acting as templates as the cycle repeats.  

The great thing about this is that every other RNA chain born is a copy of the original, but with slight, or sometimes major variations due to random copying errors. This means that true Darwinian evolution - descent with modification, acted upon by selection - can operate on RNA chains.

When suspended in water, without free floating nucleotides, the attraction between bases will cause an RNA chain to bend in on itself and stick together in certain areas as base pairs form. The end result is a complex 3 dimensional shape. Depending on that shape, it might not really do anything of interest but it might act as a weak ribozyme for a given function, it might act as strong ribozyme! 

The important thing to realize here is that the sequence of nucleotides in the RNA chain determine what kind of 3 dimensional shape and function the chain will have once folded. Any change in sequence can result in a change of the 3 dimensional shape. Changes in shape can change a ribozyme’s function.

This means that as RNA chains reproduce with modifications, natural selection can work, promoting ribozymes that happen to have survival functions, and even refining their abilities as generations pass. 

By setting up conditions allowing random RNA chains to evolve in the lab, scientists have directly observed the emergence of many powerful, finely tuned ribozymes! 

From these experiments, researchers speculate that under the right conditions, communities of evolving ribozymes could eventually give rise to living cells. 

So to sum things up, What is the RNA world hypothesis?

The RNA world hypothesis is the idea that self-replicating RNA chains were somehow produced on the early Earth. Through descent with modification, acted upon by selection, these early molecules evolved into a diversity of functional ribozymes, and eventually giving rise to living cells. 

While the basic idea of the RNA world hypothesis looks extremely promising, scientists still have many questions about the details. We don’t know for sure what pathways nature could have taken to turn simple chemistry into RNA chains. Once those first chains were formed what kinds of natural environments could have facilitated their reproduction and evolution? RNA evolution works great in a sterile lab, but could anything interesting happen in a puddle or a tidepool? 

Slowly but surely, answers to these questions and many others are being discovered by curious minds around the globe.

True claim from Evolution 2.0 - The Genetic Code is Literally a Code

This is the second 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, chapter 7 is titled "Why the Genetic Code Is a Code, Not Merely Like a Code"

In this chapter Marshall explains that the genetic code is literally a symbolic language, just like binary code is a symbolic language. He tells stories of atheists debating him online who try claiming that the genetic code is not really a code, but instead, simply seems code-like. While biologists all agree the genetic code is a code, in my own work teaching genetics and evolution I've also seen laypeople try to downplay the significance of the genetic code in a similar manner. I sympathize with Marshall's frustration. This is an important chapter in his book.

For those of you who are not familiar with the genetic code, you'll find it worth while to take 5 minutes to watch this animation called "What is DNA and how does it work?". In it, you will gain a fundamental understanding of how the code operates.

Marshall's claim in this chapter that the genetic code literally counts as code is absolutely correct. The genetic code truly is a symbolic language. Every three letters in a gene sequence act as a symbol which a ribosome reads and translates into an amino acid. In the code chart below, for example, we see that GGG codes for glycine (highlighted in blue). About this Marshall writes:

Note that GGG is not literally glycine, because the GGG nucleotides never end up in the glycine. Instead, the nucleotides merge back into the original DNA strand after it is read. GGG are the symbolic instructions to make glycine. The cell’s machinery reads these instructions and obeys them. (Perry Marshall, Evolution 2.0 page 56)

In summary, while there are many things I disagree with in the book, Marhsall's claim in chapter 7 that the "genetic code is a code, not merely like a code" is completely accurate. Biologists have accepted this and have been teaching it since 1961 when the first codon was discovered by Nirenberg's group. The genetic code fits every requirement of a language. In this case the language allows for communication between three types of RNA: messenger RNA (as shown in the animation), transfer RNA (not shown in the animation), and ribosomal RNA.

This is the second 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.

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Review of Perry Marshall’s Book EVOLUTION 2.0

Perry Marshall is a gifted writer, a clever internet marketer, and a man who believes that Jesus Christ authored the genetic code. A few months back, Marshall sent me a copy of his book, Evolution 2.0; Breaking the Deadlock Between Darwin and Design, and asked if I would read and review it. Besides writing the book, Marshall has also put forth a challenge to the world claiming he will give millions of dollars to anyone who can prove that code can be generated without an intelligent designer. As you might expect, the challenge comes with some cleverly designed caveats enabling him to easily avoid having to pay. Below I give you the first section of my review of his book. In later posts I’ll write about his challenge. 

After reading it cover to cover (well... pixel to pixel on my Kindle app), it seems that the main point of Marshall’s book, Evolution 2.0, is to set up a god-of-the-gaps argument designed to convince us all that the existence of the genetic code points to the existence of God.

"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

If that were the only message presented in this book I would have stopped at chapter 1 and given the entire thing zero stars. I'm happy to report, however, that Marshall also makes several thought-provoking arguments in Evolution 2.0 that do deserve some attention.

Marshall’s overall writing style was pleasant to read and gives us an intimate glimpse into his worldview, personal thought processes, and his continued relationship with his brother who has fallen away from their childhood faith.

Marshall is an electrical engineer by training, not a biologist, and though there were a shocking (no pun intended) number of factual errors in the book, I did enjoy his unique perspective as an outsider to the field of biology. I especially loved his chapter on epigenetics which is possibly the best overview of the topic that I have read to date.

Because of the factual errors in the book, I can’t recommend it to readers who are new to biology. That said, those who are sufficiently well versed in evolutionary theory might enjoy Marshall’s outsider's perspective of the field. I also recommend this book to science educators who would like to stay up to date on the kinds of arguments that are currently being put forth by the anti-evolution movement. In general, Marshall is not anti-evolution. He accepts common ancestry and that natural causes are responsible for the bulk of what we see in biology. That said, what I see as the main thesis of his book is nothing more than a tired, old, god-of-gaps argument, similar to those we've been hearing since Darwin first published his theory in the mid 1800s.

Just to be clear, I see no problem with scientists believing in God and even being inspired by their theology to motivate their research. For this reason (though I don't subscribe to their beliefs) I have been a long time supporter of Biologos.org and what they call theistic evolution—the idea that through faith, a person can continue to believe that God is behind all of creation while simultaneously accepting the science of biology without having to censor it. 

Unlike the faith taught at Biologos, Perry Marshall's faith seems to depend directly on some sort of evidence that God exists. In the book he says:

"...if science really told me that no God, no plan, no intentionality was needed for me to have a wonderfully engineered hand at the end of my arm, then I would make a massive, wholesale change in my belief system." page 7

Though I don't want to put words in his mouth, he seems to be saying here that if there is no evidence of God or miracles, he will become an atheist. This is interesting. With this perspective you might expect that he, and others who think like him, would be actively seeking positive evidence for the existence of God—something that could be observed, documented, and presented to the scientific community for critical review. I would personally love to be presented with positive evidence that God exists and that through Jesus I might have a chance to survive death. Likewise, I think it would be wonderful to be presented with positive evidence that aliens built the pyramids. Instead though, I cringe time and again as I hear creationists and alien believers continually take the lazy way out and think they're somehow being profound: "science doesn't know how such and such happened, therefore aliens/God did it!"

Like many creationists before him, instead of searching for positive evidence of God's existence, Perry Marshall has found what he thinks are gaps in our scientific knowledge, filled those gaps with God, and is content to claim victory for Jesus until someone can prove a natural solution to his favorite unsolved mystery. Oddly enough, in conversation with me on twitter, and in chapter 24 of his book, Perry Marshall specifically claims that he's not making a god-of-the-gaps argument because of the fact that he's offering money to anyone that can fill his favorite gap with a natural cause instead of God. The mental gymnastics on display here are simply amazing.

Though I see huge problems with the main argument put forth in this book, I give it 2 solid stars out of 5. If factual errors were corrected, I'd give it 3.

In the next few posts I will present and comment on several of the claims Perry Marshall puts forth in Evolution2.0:

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Claim #1: The genetic code is not analogous to code, it literally is a code

Claim #2: The rules of a language are always defined in advance

Claim #3: All codes whose origin we know are designed

Claim #4: You must have code before evolution can work (post coming soon)

Claim #5: Mutations are not random (post coming soon)

Claim #6: Biology teachers should emphasize transposition, horizontal gene transfer, epigenetics, symbiogenesis, and gene duplication instead of point mutations. (post coming soon)

Claim #7: Cells are intelligent (post coming soon)

Claim #8: Complex error correction systems had to exist before evolution could happen (post coming soon)

Claim #9, the big kahuna: Jesus Christ authored the genetic code (post coming soon)

(updated 5/24/2016 at Perry Marshall's request that I mention chapter 24)