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:

Next Post In Series >>

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)

What came first, the chicken or the egg? Evolution chimes in!

The theory of evolution solved the chicken or egg conundrum a long time ago... well, it did as long as the egg doesn't have to have come from a chicken: 

I got this cool graphic from my old neighbor's facebook 
page. Thanks Josh! He got it from a guy named James 
who got it from... who knows, maybe he made it?

Animals appear to have been producing eggish-like structures since at least the end of the Precambrian era where sea sponges got their start. Eggs similar to those found in modern chickens first evolved as one group of reptiliomorphs left the water, eventually giving rise to modern reptiles, birds, and mammals.

When we look at the history of life on Earth, we don't see clear signs of vertebrates on land until roughly 395 million years ago. At that time we start seeing track ways, possibly of fish beginning to come onto dry land for short periods of time.

Photo by Grzegorz Niedzwiedzki, shamelessly jacked from
National geographic's website without any sort of permission.
Long live the internet! 

And at about 375 million years ago we actually find bones of walking amphibian-like fish.

By Eduard Solà, CC BY-SA 3.0, from wikipedia

Early walking vertebrates appear to have been fully dependent on water for laying their jelly-like eggs as amphibians and fish still do today. Some frogs can lay eggs on land in extremely humid environments but without intense moisture, amphibian eggs dry out and die. This, in part, is because amphibian eggs lack an outer shell and a few membranes around their embryos. Fish, salamanders, and frogs lack the amnion, for example, one of several sacks that surround all reptile, bird, and mammal embryos as they develop.

Some frogs lay on land but only in humid environments 

As reptiliomorphs began evolving from their amphibian ancestors and moving further and further from bodies of water, selection pressure for egg survival in dryer environments appears to have increased, favoring any modification that happened to prevent eggs from drying out. The eggs of modern reptiles and birds with multiple internal sacks and a relatively tough, dry outer shell was the end result (though modern reptile and bird eggs do vary in shell hardness from species to species). 

When chickens began evolving sometime after the extinction of their non-avian dinosaur cousins, they were already using shelled eggs. So what does all this mean? What actually did come first, the chicken or the egg? The egg of course, by many millions of years!

I must add however, that my answer is null if you add a rule to the question saying the egg only counts if it was laid by a chicken. With that rule in place, the chicken had to come fist, but that's a stupid rule.

So that's that!
Jon Perry

P.S.
Here's a bunch of videos of different species of fish coming out on land for a brief stroll. Those little buggers are still at it! 

David Attenborough vs Crazy Land Shark!

Mud-skipper fight!

Lungfish are cool

Fish climbs waterfall with it's bare fins!

Awesome! Now I have a blog!

Today at 12:56 in the morning, I decided that I need a simple blog where I can write my thoughts about biology, review books, and jabber with my fingers about stuff I think is cool. Here it is. If you happen like my brain spillings, that's great.