Friday, March 29, 2013

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


Parsimony Principle

          Parsimonious means stingy. But in the sense of fitting species to a taxonomical tree, it means the ‘best fit’. Again, we know that there exists a single unique tree which can be obtained by cladistic taxonomy. It is not easy to find the cladistic tree. So, finding a tree which is very similar to the cladistic tree would be much easier. The parsimony principle here is in the sense that the difference from the cladistic tree must be as little/stingy as possible.           
          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.’


“The most parsimonious tree is the tree which is ‘economically meanest’ with its assumptions, in the sense that it assumes the minimum number of word changes in evolution, and the minimum amount of convergence.”

Minimum Amount of Convergence

        Molecular classification is more reliable than trait-based classification. Behavioral similarity can cause convergence (i.e., similarity) in traits. We can be fooled by trait-based classification. 
Molecular classification does not depend on behavior. It is the pure nature embedded in each cell of organism. So, we don’t have to be worried about accidental convergence at the molecular level. 

The Difficulty in Find All the Trees

        To find a tree, you can start at the bottom of the hierarchy. Here, you first identify all possible combinations of animal categorizations. Then, you pick the one that fits the best. Next, you repeat the process for the next level up the hierarchy. This time you do not categorize the animal. You categorize the categories you’ve got from the first step.  You can repeat this process until you reach the top,  and you will get a taxonomy tree. 
        The task for finding all possible trees is really hard. There are 15 trees for 4 animals. When you have 20 animals, there are more than 8 million million million trees. The fastest computer in this world would take 10,000 million years to find identify the most parsimonious tree.

Now What?

        We can’t just do all categorization by force. We need to use our intuition to rule out combinations which make no sense. We use trait-based categorization to fasten taxonomy process. 

Types of Taxonomists

        Taxonomists can be classified into
  1. Phyleticists: They try to find a ‘family tree’ based on evolutionary relationships. The belief is that there is only one unique family tree, because there is one true history. The family which differs from the history would be the wrong one. The objective of phyleticists is to find that one unique family tree. There are two sub-groups of phyleticists which pursue the same purpose in different ways:
    1. Cladists: These people are obsessed with branching, i.e., how species branch out. But they don’t care how much a descendant differ from its ancestor. They approach is to find all possible tree sand pick the best one. By ‘the best’ one, they mean to find the tree where animals in each group has most features in common. During the classification, they give more weight to more recently developed features. 
    2. Traditionalists: These people are similar to cladists but they also care about the amount of change at each branching point. 
  2. Pure-resemblance measurers: They try to find a ‘resemblance tree’ based sole only on similarity in (molecular or traits) pattern. Since resemblance trees are not based on history, there can be many trees. The upshot of pure-resemblance measurers is that their approach work not only for living things, but also for non-living things:
    1. Pheneticists, or Numerical taxonomists, or average-distance measurers: These people are more like mathematicians than biologists. They look at everything they can, and try to create resemblance index. They then plot each species in a space (e.g, X-Y Coordinate for a two dimensional space). Similar species are placed close to each other. Finally, they apply some kind of fitting model to define clusters of similar living thing. 
    2. Transformed cladists: These people use the same technique as what the cladists do. But they do not care about ancestor. Some of them even assume that there is something wrong with evolution, and taxonomy would be better without evolution. 


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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.

CH9: Puncturing punctuationism




          Evolution is like slowly filling a bottle with water. You can constantly fill the bottle. Alternatively, you can quickly fill the bottle, stop for a while, and start filling again. Either way, in the end, the bottle is filled with water. For evolutionists, the former and latter approaches are referred to as  ‘gradualism’ (constant speed) and ‘punctuationism’ (variable speed), respectively. 


Gradualists and Punctuationists


          Gradualists believe that evolution proceeds constantly and slowly. Punctuationists, on the other hand, believe that evolution consists of two alternating periods. In an evolving period, things evolve significantly. In a stasis period, nothing evolves at all. 

Macro Mutation

          Macro mutation is a large scale mutation. The mutants would greatly differ from the original species. 

Tuesday, March 26, 2013

CH8: Explosions and Spirals


Feedback System and explosion


A feedback system is a system where the output is fed back to the system as an input. There are two main types of feedback systems: Negative and positive feedback system. In a negative feedback system, the amount of feedback input decreases as the output increases. It is very useful to control the system at an optimal level. 


  
On the other hand, the feedback input in a positive feedback system increases as the output increases. The input accumulates even with a small increase in output. It is this accumulation which will lead to explosion in the end.

Positive Feedback and Sexual Selection: Female’s whim v.s. Male’s Ornament




  


Friday, March 22, 2013

CH7: Constructive evolution


Natural Selection and Mutation

Natural selectionism is a destructive process where it removes bad things. Mutation, on the other hand, adds things to create new possibilities. Together, natural selection and mutation comprise evolution.


“There are two main ways in which this build-up can happen; The first of these goes under the name of 'coadapted genotypes'; the second under the name of 'arms races'. The two are superficially rather different from one another, but they are united under the headings of 'coevolution' and 'genes as each others' environments'.”

Tuesday, March 19, 2013

CH6: Origins and miracles

          The theory of the blind watchmaker rests on replication and cumulative selection. It works through generations to churn out better offsprings. Admitting this fact, one might still wonder what is it at the beginning? What is it before life began? In this chapter, we shall explore the answer to this question. 

How Improbably is Really Improbably?

Probability

           Is it one in 1040? Even if this odds is very small, it’s still measurable. There are other odds, say one in 1045 or one in 10450, which is less likely. The question here is how improbable would be equivalent to impossible? In particular, this is the question we’d like to answer:
“how much luck are we allowed to assume in a theory of the origin of life on Earth?”

Miracle

          For most of us, a miracle is something quite impossible. We can’t imagine a miracle happening to us. But for mathematicians, a miracle is merely something highly improbable.

The Birth of Life

           We know, from traditional wisdom, that a planet is originated from compound gas. So, we would like to know the chance of these compounds to form a self-replicating molecule. From that point, cumulative selection will take over, and the self-replicating molecule will evolve into a life form. 


Chemists

          Our first intuitive idea is to turn to the chemists. We can ask ‘How likely does a compound turn into a replicator molecule? If we consider all possible combinations of compound. It could be something like one in billion billions. How improbable this is? If you try to covert a compound every second, it will take one billion billion seconds or 31.7 billion years to get a single replicator molecule. 

How Long is One Billion Years?

           A chemist tends to thinks that a period of billions of years is way too long. No chemist would ever live to see  compound-to-replicator conversion. They would tend to say that this is impossible. No chemist known to our world would live to see the entire conversion process. 
          But, mathematically, the probability is non-zero. Even if the chance is very vey slim, it can happen if you wait long enough. And, 31.7 billion years are not very long comparing to the life of universe. 

Creating a Lifeform

Organic Chemistry

          Chemists divide their fields of study into organic Chemistry and non-organic Chemistry. The former deals with carbon, while the latter deals with the rest of the elements. Carbon is related to living things, because it is found in living things and because it has property suitable for living things.

“The essential property of carbon atoms that makes them so suitable for life and for industrial synthetics, is that they join together to form a limitless repertoire of different kinds of very large molecules.”


Can a Chemist Create a Lifeform?

          So far, chemists have failed to recreate life. But, we should be more worried if they succeed doing it in a few centuries, rather than tens of millions of years. Why? Well, if humans can create humans, all sorts of problems will follow. How? I’ll let you figure it out. 

What If Someone Can Create a Lifeform?

          Let’s assume for a sake of argument that a life form can be created within a few centuries. Comparing to the life time of the universe, a few centuries is very very short. Then life form must have existed in a lot of place the universe. And, that life form should have a technology to contact us already. But so far, except for urban legends, we have not seen any extra terrestrial at all, right? 
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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.

Friday, March 15, 2013

CH5: The Power and The archives 2/2



Genetic Information in Our Body

Why Do We Read Genetic Information?

          There are generally two purposes to read from a memory: Copying and taking actions. When multiplying, the original cell copies its DNA to the descendent. Taking action is the process of ‘DNA translation’, where our body reads (i.e., translates) information stored in DNA in order to create a particular type of protein. 

 Forming  Protein

          To translate DNA to protein cell, first, DNA must be translated to RNA. Our body then follows the RNA instruction to create polypeptide (a.k.a., protein or poly amino acid). Again, DNA is NOT transformed into protein. Instead, it contains the instruction of how amino acids should be assembled and from a specific kind of protein. That’s why the process is called ‘DNA translation’, not ‘DNA transformation’.


Protein and Amino Acid

          Amino acid is a biologically organic compound consisting of carbon, hydrogen, oxygen, and nitrogen. There are about 500 known amino acids, each having different construction of the four basic elements--‘A’, ‘T’, ‘G’, and ‘C’. Out of these 500, only 20 amino acids are in living cells. A protein is a chain of one of these amino acids. After the formation, the chain coils up to a knot. The shape of a knot is uniquely determined by the sequence of amino acids. Therefore, the protein is also referred to as poly amino acid. 
       The sequence of amino acids, and thus the protein shapes, is determined by a three-letter symbol called a‘genetic code’ in DNA. Again, each letter in DNA can be either ‘A’, ‘T’, ‘G’, or ‘C’.  So there are 4 x 4 x 4 = 64 possibilities for a given symbol. It is this symbol which governs how a certain amino acid is formed. But, again, there are only 20 possible amino acid in living cells. So the translation from a genetic code to protein shapes (i.e., amino acid) is many-to-one translation. 


Enzyme and Cells

There is a special type of protein molecules called ‘enzyme’. Enzyme is a machine which creates a particular type of chemical products. This product gives a cell its individual shape and behavior. Since DNA determines the sequence of amino acid, it determines the type of enzyme and therefore the shape and behavior of cells. 


Same DNA,Different Functionalities

Every cell in our body contains the same DNA. But why does each cell act differently? For example, why does liver cells differ from kidney cells? The reason is that not all cells read DNA in the same way. When  DNA are read differently, the resulting protein shape is different and the cell is different.
If we trace back one step, we might ask ‘Why does cell read DNA differently?’ The answer is that the way DNA is read depends on the chemicals in the cell. Since the chemical level in a certain cell are not uniform, when the cell splits, each daughter cells would have different chemicals. So, they read DNA in a different way and so. This final result of DNA is visible in, for example, eye color, hair thickness, and so on. 
genetic information and natural selection

Vertical and Horizontal Transmissions

      DNA can be transmitted vertically or horizontally. Vertical transmission is a REPRODUCTION process. It is an act of copying DNA from one generation to the next, without any change. It is like copying a book from an archive. This is why we sometimes call DNA already in place ‘archival DNA.’ We call the path where the DNA is passed on, from our ancestors to our children, a ‘germ line’.
      Horizontal transmission is when DNA influence a creating of a cell via RNA. It is the process of DEVELOPMENT.

Reproduction

      DNA coils up into a ‘chromosome.’ Each human cell has 46 chromosomes, with the exception of reproduction cells. All regular cells are identical in addressing and contents. Reproductive cells (e.g., sperms and eggs) randomly took 23 contents from all 46 we have. When sperms mates with eggs, two 0f 23 chromosomes combine into 46 chromosomes in an embryonic cell. This cell multiplies, and the 46 chromosomes we inherited from our parent are copied to the new multiplied cells. 

Vying to Exist

Rival DNA and Natural Selection

      Natural selection is about how ‘rival DNA’--A particular content which shall replace the current content in a particular address--gets itself vertically transmitted into archival DNA. The vertical transmission depends on how well the DNA is transmitted horizontally to take action which fosters the ability to survive.


Durability and Generatability

      Things exists because it has ability to survive. This ability consists of durability and generatability. Durability is an ability to withstand the environment, at least long enough until generatability kicks in. Generatability is an ability to reproduce itself. DNA has poor durability but great generatability. The contents it stores constantly fade,  and must be regularly refreshed by the hosting organism.  Durability and generatabiity complement each other to preserve DNA information for millions of years. 

Mutation and Natural Selection

      Mutation is in fact to only way to evolve. If DNA did not make any error in copying, we would ALWAYS be the same. We would not be better nor worse in surviving. The the fastest we can evolve is therefore no greater than the rate of mutation. Natural selection, on the other hand, slows down the rate of evolution, because it throws away any mutation that degrades the ability to survive. 


Properties for Existence

      Anything that exists needs to have three properties
  1. The ability to self-replicate (hence, the thing is called a ‘replicator’): This is an ability to copy/populate itself. A replicator use instructions stored in a template to create a replica from raw material. 
  2. Random error in copying:  Error is essential for evolution. With our random error, the replicator would remain unchanged. It wouldn’t be able to adapt to changing environment. 
  3. Ability to exert power over their own future: Each property of a replicator should have different probability of being replicated. A replicator should be able to keep good properties and throw away bad properties. 


The Blind Watchmaker

The above three properties for existence are not attributed to a particular organism. They are general condition for any natural things. The natural selection is blind. It is the blind watchmaker.
“It is all utterly simple and automatic. It is so predictable as to be almost inevitable.”
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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.

Tuesday, March 12, 2013

CH5: The Power and The archives 1/2



Digital Information

A bit is a storage unit in a typical digital information system. Its value could be ‘0’ or ‘1’. A storage unit in genetic information system is a nucleotide, and its value ranges from ‘A’, ‘T’, ‘G’, to ‘C’. So each unit of storage can store four possible values. 

 Genetic Information

Polymerization is an act of joining polymers to create a very very long chain. When nucleotides are polymerized, the result is called ‘polynucleotides’. Living cells have two kind of polynucleotides: DNA and RNA. So DNA and RNA, or more broadly polynucleotides, are data structure capable of containing genetic information.
Our DNA and RNA are capable of storing staggering amount of information. But our body uses only 1% of DNA and RNA. To dates, nobody knows what the other 99% of DNA and RNA is for.

ROM and RAM

In a computer, ROM (Read Only Memory) is a type of memory that you can write to it once. Afterward, it can only be red. RAM (Random Access Memory), on the other hand, allows you to read and write to it as much as you want.

Friday, March 8, 2013

CH4: Making tracks through animal space



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Evolution of Organs

     Every human part is complicated. Take human eyes for example. It is less plausible to develop an eye from something radically different in one step. It is more plausible that we develop our eyes though millions of changes.


    From this argument, it is reasonable to assume that, at the beginning, we don’t have an eye. But better eyesight  helps us a little more in surviving. We gradually develop our eyes. Our eyesight become sharper though generation.  Up to some point, we can see sharper images and differentiate a tiger from a cat.
Despite the use of eyes as an example, the above fact is true for every organ such as ears, wings, venom glands. All organs evolve slowly. For example, 1% of hearing is better than no hearing at all, and 2% of hearing is better than 1% of hearing. The chance of survival increases continuously as each organ improves, no matter how small the change is.