Tuesday, April 2, 2013

CH10: The One True Tree of Life (1/2)

Library and Biological Taxonomy

          Taxonomy is a science of classification. Library classifies books for convenience. There can be several ways for classification such as subject-based or alphabetical. All these classifications equally makes sense, and make the access to the books more convenient. 
          Biological taxonomy can also be based on various criteria. But, the single way which stands out is based on evolution relation. Biologists call this method ‘cladistic taxonomy.’

“What it does mean is that there is no single classification system which, in a world of perfect information, would be universally agreed as the only correct classification. The taxonomy of living creatures on the other hand, as we shall see, does have this strong property that the taxonomy of books lacks; at least it does if we take up an evolutionary standpoint.”

Cladistic Taxonomy

         This taxonomy is based mainly on cousinship. It is a hierarchical classification. Each node in the hierarchy represents a species. Upper levels represent ancestors, while lower levels represent descendants. 
          True cladistic taxonomy has a remarkable property. Once branching out beyond a certain minimum distance,  the species will never converge again. They will all diverge.

Perfect Nesting

          Let’s pull out a paper and a pen. Write down all the names of animals. Draw a circle around similar animals, e.g., tiger and lion. Then draw a bigger circle to cover broader classification, e.g., cat around the previous circle containing tigers and lion. 
          The surprising is that every circle will lie completely within a larger circle. No circle would partly overlap with each other (although we have bacteria as an exception). 
      We don’t see this property in taxonomy of other things. For example, there is always intermediate book sections such as history and theology, politics and economics. We don’t see that intermediate in living creature. That’s why the nesting is ‘perfect.’

“... the problem of intermediates is inescapably, inherently a part of all taxonomic systems other than that which springs from evolutionary biology.”

Reasons for Incomplete Cladistic Taxonomy

          Cladistic taxonomy provides perfect agreement in the world of perfect information. The reality has two qualities which prevent us from doing completely cladistic taxonomy: 
  • Imperfect information: We don’t have enough fossil to tell who is actually the ancestor of a certain species.
  • Too much information: When we include too many creatures, especially those in the ancient, species become blurry. Here, we can’t draw a solid line between two species.  

Convergence Problem

          Again, with this perfect taxonomy, no two species, once branching out, would converge and create an intermediate categorization problem. 

Accidental Convergence

          Adaptation can create convergence problem.  Different species with similar way of life in different part of the world can have very similar traits. By looking at these traits, we tend to think that these species share the same ancestor. In the perfect nesting exercise, we tend to put these two species in the same circle. This will later on create perfect nesting violation, where a circle may partly overlap with another circle. 

Molecular Biology

          Molecular biology is another way we can use to classify living things. Unlike trait-based classification, molecular biology inspects living things at the molecular level. You may have accidental convergence from trait-based classification. But you do not have the same problem when using molecular biology. In fact, you can even quantify the difference between two species by using molecular biology. 

Genetic Dictionary

          The instruction which translates information in DNA into protein is referred to as ‘Genetic Dictionary.’ It consists of only 64 DNA words, and each word has exactly three letters. It turns out that all living things uses almost the same dictionary in all the protein translation process.

“The genetic code is universal.”

          The difference in each species is the information stored in the DNA. If a genetic code is a word, an amino acid will be the meaning of a word. And, a protein consisting of amino acid will be a sentence. 

“Though all living things share the same dictionary, they don't all make the same sentences with their shared dictionary.”

Quantifying Similarity

          Unlike traits, protein sentences are not guided by natural selection. In addition, they are unique to each species. We can compare how the similarity of two protein sentences belonging to two species. Then, we can use this quantified similarity to tell how close these two species are. By using molecular biology, we will never have to be misled by accidental traits convergence again.

“The beauty of modern molecular biology is that we can measure the difference between two animals exactly, as the precise number of words by which their versions of a particular sentence differ.”

Species Ambiguity

Qualification Words: No Solid Line

          Short and tall are qualification words. We can’t always tell how short is short and how tall is tall. What we can do is to compare two people whose height differs greatly. In such case, we can tell which one is short and which one is tall. We can’t draw a solid line between two opposing qualification words. These words become meaningful when  there is no intermediate between two ends.  

Is There Any Line for Species

          Similarly, we are able to differentiate humans and chimpanzees, because the intermediates between these two species have all become extinct. 
          The conventional wisdom believes that we, humans, develop from chimpanzees. We have made small cumulative change for a very long time, and we have become who we are today. Now, imagine if there still exist all intermediates, i.e., all evolved creatures from chimpanzees to humans. Then we will be in big trouble. How do we draw the line between humans and ‘evolved chimpanzees?’ What sort of right should humans have? What sort of right should ‘evolved chimpanzees’ have? How are we going to find names for all evolved version of chimpanzees?   Environment refers to the surrounding condition.   Animals which can deal with predators and climate better will live longer. Similarly, genes which deal with the environment better tend not be eliminated by natural selection.
           So, what does ‘environment’ mean to genes? A gene is usually surrounded by genes. So, genes which deal with other genes better will be more likely to reproduce.
So genes do not evolve individually. They evolve as a team. Once a team has advantage edge, it is hard for other teams to break in, even if the other teams are more efficient.
Book or Audiobooks?

Personally, I prefer audiobooks. It's fun, and I can listen when I'm doing something else. It also makes other activities (e.g., jogging) a lot more fun. For more detail about audiobooks, please read [this post].

There is one more reason that may encourage you to go for the audiobook version. You can get it now for FREE. Audible offers you a free trial for 14 days. Even if you get the book and cancel the subscription right away (so that you don't have to pay), you can keep the book. And, don't worry if you lost the audiobook file. Just log into audible.com. You can keep downloading the over and over again.
About the summary: It takes time to finish up a book. And, when you do, sometimes, you want to review what you learn from the book. If you do not make  notes as you read, you might have to go through the book once again. This can be time-consuming when you are dealing with a book. But you can still flip through the book and locate what you are looking for.

However, when the material is an audiobook, it is extremely hard to locate a specific part of content. Most likely you will have to listen to the entire audiobook once again.

This book summary will help solve the pain of having to go through the book all over again.

I am leaving out the details of the books. Most books have interesting examples and case studies, not included here. Reading the original book would be much more entertaining and enlightening. If you like the summary, you may want to get the original from the source below.

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