Evolution and Genetic Science

Evolution and Genetic Science, Critical review of creationists ranting! 1

Evolution & Genetic Science

Asathoma Sath Gamaya, Thamosama Jyothir Gamaya, Mruthyorma Amrutham Gamaya From lies to Truth, From Darkness to Light, From Death to Eternity

Araf Karsh Hamid

Evolution and Genetic Science, Critical review of creationists ranting!

2

Personal incredulity of pseudo scientists has reached a state where they poised to sabotage the current education system across the world. I submit this document to the students who seeks wisdom and not pseudo science. This is a critical review of N M Hussain’s article titled “Evolution and Genetic Science” published in (Malayalam) the magazine Sneha Samvadham on October/November 2012. The focus of N M Hussain’s article is to prove that the Darwin’s Evolution theory has failed in the last 150 years, and this failure results in Creation (by God) as the only alternate solution. This document analyzes N H Hussain’s arguments and check if he has provided scientific facts to disprove a 153 years old theory or his opinion is biased towards Creationism or Intelligent Design. Apart from that, this document focuses on show casing evidence (empirical data) across a wide spectrum of domains to support evolution. Even though this article started with the review of Hussain’s article, the scope of this article evolved into a state where it gives a summarized, still holistic perspective on evolutionary biology and alternate religious views (Creationism and Intelligent Design). I have sited more than 150 reference points (to get deeper into each area) and more than two dozen books to refer on various subjects like Evolutionary Biology, Neuro Science, Quantum Physics, Relativity, and Morality etc., and videos lectures from prominent universities and medical institutes. It was the best of times, it was the worst of times, it was the age of wisdom, it was the age of foolishness, it was the epoch of belief, it was the epoch of incredulity, it was the season of Light, it was the season of Darkness, it was the spring of hope, it was the winter of despair, we had everything before us, we had nothing before us, we were all going direct to Heaven, we were all going direct the other way....(Hell) ~Charles Dickens -‐ "A Tale of Two Cities". Reviewed Article Oct, 2012 Evolution and Genetic Science by N M Hussain, Sneha Samvadham Reviewed By Oct, 2012 Araf Karsh Hamid © Copyrights on images and other references in this document This document is purely for education purpose only and not meant for any profit. The copyrights of images and other references used in this article belong to respective web sites, articles and books.


Table of Contents

Introduction -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 6 Understanding the structure of this document -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 8

1. Understanding Evolution -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 9 1.1 History of Earth -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 9

1.1.1 Figuring out Earth’s age -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 9 1.1.2 Geological Time Periods (from BBC) -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 12 1.1.3 Geological Time Line (from BBC) -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 12 1.1.4 Tree of Life (from BBC) -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 13

1.2 Understanding Darwin’s Theory of Evolution -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 18 1.2.1 Idea 1 – Natural Selection -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 18 1.2.2 Idea 2 – Common Descent (Descent with Modification) -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 18 1.2.3 Idea 2.1 – Single Origin of Life -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 18 1.2.4 Idea 3 – Variation in Rate of Change -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 18 1.2.5 Natural Selection -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 19 1.2.6 Refuting Creationist claim that Natural Selection Doesn’t Work -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 20 1.2.7 Misconceptions about Evolution Theory -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 22 1.2.8 Predictive Power of Evolution -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 23

1.3 Understanding Genome – DNA, Chromosomes, Genes & Alleles -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 24 1.3.1 DNA -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 24 1.3.2 Mitochondrial DNA -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 26 1.3.3 Chromosome -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 27 1.3.4 Gene -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 28 1.3.5 Allele -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 29 1.3.6 Control Genes -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 29 1.3.7 Gene Pool -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 30 1.3.8 Comparing Genotype and Phenotype -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 31 1.3.9 Amino Acids -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 32

1.4 Mutation -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 33 1.4.1 Where do mutations occur? -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 33 1.4.2 Kinds of Mutation -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 34 1.4.3 Mutation Models -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 34 1.4.4 Types of DNA Mutations and Their Impact -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 38 1.4.5 What causes mutations? -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 39 1.4.6 What are the consequences of mutations? -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 39

1.5 Natural Selection at Genetic Level -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 40 1.5.1 Neutral Theory: The Null Hypothesis of Molecular Evolution -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 40 1.5.2 Positive Natural Selection -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 41 1.5.3 Negative Natural Selection -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 42

1.6 Historical Background on Darwin’s Theory of Evolution -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 43 1.6.1 Pre Darwinian Theories -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 43 1.6.2 Refuting Creationist claim on Darwin’s history -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 44

1.7 FARM Formula to test Evolution Theory -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 45 1.7.1 Refuting Creationist claim on Natural Selection: Analyze geological time -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 46

1.8 Comparing Two Religious Views against Science (Evolution) -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 47 1.8.1 Creationism -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 48 1.8.2 Intelligent design (ID) -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 48 1.8.3 Irreducible Complexity (IC) – By Michael Behe -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 48 1.8.4 Bacterial Flagellum – Fallen case of Irreducible Complexity -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 49 1.8.5 Specified Complexity (SC) – By William Dembski -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 51


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1.8.6 Example using Dembski Explanatory Filter to detect Design -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 52 1.9 Verdict of prominent cases of Creationism Vs. Evolution in US Courts -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 55

1.9.1 Supreme Court of the United States, Epperson v. Arkansas, 1968 -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 55 1.9.2 Supreme Court of the United States, Edwards v. Aguillard, 1987 -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 55 1.9.3 Kitzmiller v. Dover Area School District, 2005 -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 55

2. Wrong interpretation of Science and Scientist’s Quotes -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 56 2.1 Stephen Jay Gould, Niles Eldredge -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 56

2.1.1 Refuting Creationist claim that Evolution is dead as per Stephen Jay Gould -‐-‐-‐-‐-‐-‐-‐ 56 2.2. Steven M Stanley -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 58 2.3 Theories to explain the progress of Evolution -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 60

2.3.1 Punctuated equilibrium -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 60 2.3.2 Multiple meanings of gradualism -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 60 2.3.3 Quantum evolution -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 61 2.3.4 Creationist interpretation on Gould’s Punctuated Equilibrium Theory -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 62

2.4 Motoo Kimura -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 65 2.5 Theories on Molecular Evolution -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 65

2.5.1 Population genetics -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 65 2.5.2 Genetic Drift Vs. Natural Selection -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 66 2.5.3 McDonald–Kreitman test -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 66 2.5.4 Neutral Theory of molecular evolution -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 67

2.6 Theodosius Dobzhansky -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 68 2.7 Genetics and Origin of Species -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 68

3. Evidence for Darwin’s Theory of Evolution -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 70 3.1 Micro Evolution Evidence -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 70

3.1.1 Evidence for Evolution in Human Time Frame: Malaria Vs. Homo Sapiens -‐-‐-‐-‐-‐-‐-‐-‐-‐ 70 3.1.2 Fighting the evolution of malaria in Cambodia -‐ Berkeley University -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 72 3.1.3 E. coli caught in the act of evolving -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 72 3.1.4 Chromosome 2 in Human DNA -‐ Evidence for Common Descent -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 74 3.1.5 Endogenous Retro Virus – Evidence for Common Descent -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 75 3.1.6 Molecular Clocks: Protein Evolution -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 76 3.1.7 Cytochrome C -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 78

3.2 Interpreting the Fossil Record -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 79 3.2.1 Paleontology -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 79 3.2.2 Paleoanthropology -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 79 3.2.3 Taphonomy -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 79 3.2.4 Doing math with species and fossils -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 79

3.3 Macro Evolution Evidence -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 80 3.3.1 Evaluating the Design of Giraffe -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 80 3.3.2 Evolution of Italian Wall Lizards -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 81 3.3.3 Evolution of Whales: From Land Animal to the Giant of the Ocean -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 81

3.4 Transitional Fossils -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 85 3.4.1 Tiktaalik: Fish to Tetrapods (Amphibians, Reptiles, Mammals) -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 86 3.4.2 Thrinaxodon : Reptiles to Mammals -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 87 3.4.3 Archaeopteryx : Reptiles To Birds -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 88 3.4.4 Ambulocetus : Land Mammals To Ocean Giant -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 89 3.4.5 Quadrupedal Primates to Bipedal Primates -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 90

3.5 Final nail in the coffin of the creationists -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 93 3.5.1 Three stages of Evolutionary Biology -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 93 3.5.2 Creationists buried for ever -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 94

4. Conclusion -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 95


4.1 Summarizing the critical mistakes from the article -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 95 4.2 Analyze Creationism, Intelligent Design and Evolution -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 96

4.2.1 Analyzing the Micro and Macro Evidence -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 96 4.2.2 Analyzing Intelligent Design -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 96 4.2.3 Analyzing Creationism -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 97 4.2.4 Questions to Creationists and Intelligent Design Proponents -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 97 4.2.5 Some more interesting questions to creationists of Abrahamic faith. -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 98

5. Explore (Videos and Books) -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 99 5.1 Glossary -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 99 5.2 Videos -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 100

5.2.1 Evolution and Genetics -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 100 5.3 Websites on Evolution -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 100

5.3.1 Universities -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 100 5.3.2 Web Sites -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 100

5.4 Books -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 101 5.4.1 Cosmology and Quantum Physics -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 101 5.4.2 Evolution and Genetics -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 101 5.4.3 Neuro Science -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 101 5.4.4 Others -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ 101

What is Science? By John A Moore, 1993

A way of Knowing By:

• Accumulating data from observations and experiments • Seeking relationships of the data with other natural phenomena • Excluding super natural explanations and personal wishes

Science is never complete, and each new discovery produces new questions.

By Thomas H. Huxley “Science is nothing but trained and organized common sense”

Science: • A body of Knowledge • The process for building that Knowledge • Has both creative and critical components


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Introduction Fighting against Darwin’s Evolution theory has a long history as old as the theory itself. However, what’s surprising is you don’t see creationists fight against other fields of science for example Theory of Relativity or Quantum Physics which is much more bizarre, than saying we got evolved from Ape. Compare to Relativity and Quantum Physics, saying we were evolved from Ape is nothing. But still why this massive amount of century old attacks against biology. Here is the answer for that

That describes everything from the motion of the planets to galaxies to the color of your skin. Now do you think any creationist will dare to question any of these things? The answer is a big NO. The latest book from Stephen Hawking “The Grand Design” says there is no role for a Supreme power for the Big Bang of the Universe and its functions, the latest book by Laurence M Krauss says, Universe came from nothing. Last year (Oct 20111), three scientists were awarded Nobel Prize for confirming the expansion of the Universe, confirming Big Bang Theory. Oh boy!, its expanding at a faster rate than anticipated due to Dark Energy. That’s the second evidence for Big Bang Theory. Prior to this Scientists got Nobel Prize in 19782 and 20063 for Cosmic Microwave Background Radiation4, the remnants of Big Bang.

The big-‐bang theory predicts that this primordial light should display a classic “blackbody” spectrum, an indicator that the whole universe started out at a uniform temperature before

1 Nobel Prize for Physics 2011 2 Nobel Prize for Physics 1978 3 Nobel Prize for Physics 2006 4 MSNBC – Americans win Nobel for Big Bang study March 10, 2006


expanding into the much less homogeneous state we now observes. That is exactly what COBE5 found. “It’s just a magnificent verification of the big bang,” said Lawrence Krauss, a professor of physics at Case Western Reserve University in Cleveland.

Albert Einstein published General Theory of Relativity in 1916 and the Big Bang model was a natural outcome of this theory. However, wisdom at that time points towards a static universe. So, he modified his theory by introducing Cosmological Constant to make his theory predict the static model. However, in 1929, Edwin Hubble announced the expansion of universe as he observed that the galaxies were systematically moving away from us with speed proportional to their distance. Einstein abandoned the Cosmological Constant after this observation by Hubble. However, a number of observations in 1998 points towards a cosmic acceleration have revived the cosmological constant! Even Einstein’s blunder became another brilliant idea. Following image shows the history of the universe with initial expansion due to inflation and the current expansion due to Dark Energy. 20116 Nobel Prize7 for Physics is attributed to the accelerated expansion of Universe due to Dark Energy.

I feel its time there should be some mathematical formula, which will explain the concept of Natural Selection and predict changes (from mutation, genetic drift) of any species predicting the potential DNA sequences of the future species. Once that happens blind pseudo science attack on Evolution will stop. By the way you must wondering if I understood the above formula. Absolutely Not!

5 COBE – Cosmic Background Explorer 6 CNN – Scientists studying Universe’s expansion win Nobel Prize in Physics October 4, 2011 7 BBC News – Nobel Physics Prize honors Accelerating Universe find October 4, 2011


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Understanding the structure of this document This document is divided into following sections:

1. Understanding Evolution 2. Wrong Interpretation of Science and Scientists Quotes 3. Evidence for Darwin’s Theory of Evolution 4. Conclusion 5. Explore (Videos & Books)

1. Understanding Evolution This section explains the key ideas of Darwin’s theory of Evolution. It briefly introduces the user to genetic science by explaining mutation and concept of geological time line, which is very important to understand evolution of species. The key part of evolution is variation and selection and the time frame. Variations happen through mutations and Natural Selection is the key for the branching out and diversification of species. Time is a very critical component of evolution. When we talk about time we are not talking about time in days, months or years. We are talking about time in millions of years. To explain that briefly, 60 million years ago India was an island and was not part of Asia the way we see it today. Indian island barged into Asia and that collision created the Himalayas. This gives you an idea about the geological time frame we are talking about. Understanding Natural Selection, Common descent with modification along with how mutation works, is a key part in the whole process. Apart from Darwin’s theory of Evolution this section also looks at the alternate non-‐scientific theories from creationists. Non-‐scientific theories masqueraded as scientific theories. 2. Wrong Interpretation of Science and Scientists quotes One of the tactics the creationists deploy is to misquote the prominent scientists and wrongly interpret the their theories to confuse the public. This section debunks such claims with evidence from such scientist’s latest books, press statements. 3. Evidence for Darwin’s Theory of Evolution This section showcases some of the key evidence to support evolution from fossil records, genetics, some bad designs in species and other areas of science. 4. Conclusion This section analyses every section in this document like evidences, creationist theories etc.


1. Understanding Evolution Almost every creationist’s says Evolution is just a theory and not a fact. According to "The American Heritage Dictionary," a theory is: A set of statements or principles devised to explain a group of facts or phenomena, especially one that has been repeatedly tested or is widely accepted and can be used to make predictions about natural phenomena. Let me start with N M Hussain’s understanding of Darwin’s Theory of Evolution from his article. Compared to popular belief (creationism) in Darwin’s time, Darwin made two extra ordinary claims. Before I address this let me show what Hussain wrote about Darwin’s Theory in his article titled “Evolution and Genetic Science8” in the Magazine Sneha Samvadham cover story (2012 October).

1.1 History of Earth Before we get into the article let us have a quick look at the scenario in 1859 at the time Darwin published “On Origin of the Species”.

1. Earth is too young. 2. No transitional forms in the fossil record. 3. Natural Selection can’t work because rare variants would be swamped out. 4. Animals look too different to come from common ancestors.

1.1.1 Figuring out Earth’s age According to Archbishop James Ussher’s9 estimate based on genealogy in the Bible Earth got created around the year 4004 B.C. That put the age of Earth around 6000 years old. Lord Kelvin10 (famous physicist at that time) calculated that the age of Earth is around 40 (max) million years. Kelvin’s estimate came from physics of cooling of the Earth and the Sun. Darwin felt this age has to be wrong, because with 2 to 40 million years he realized that evolution is not possible for so many diverse amounts of species you observe on planet Earth. Lord Kelvin was against the concept of Darwin’s Evolution and he felt his calculation of Earth’s age refutes Darwin’s theory of Evolution and point towards the spontaneous creation of species by God. Here is an abstract from the paper published by University of Manitoba11, Canada

“Calculations at high school level can be used to show how Newton estimated the age of the Earth from the cooling of a hot body and later Helmholtz and Kelvin applied thermodynamic arguments to finding the ages of both the Sun

8 Evolution and Genetic Science by N M Hussain, Sneha Samvadham, 2012 October 9 Archbishop James Ussher – Wikipedia 10 Lord Kelvin – Wikipedia 11 Calculating the Age of Earth and the Sun by Arthur Stinner


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and the Earth. Finding the Sun to be younger than the Earth was a puzzle until the discovery of radioactivity and the Sun’s true source of power.”

Albert Einstein’s E=mc2 revolutionized the understanding of the power source and age of the sun. 4 Hydrogen atoms – in fusion make 1 Helium atom and releases energy

Discovery of radioactivity provides new way to calculate absolute age of rocks, and detailed measurements suggest that the Earth is around 4.6 billion years old. Now this (Age of Earth) has been proven beyond any doubt in the present time. Now consider the forces Darwin faced at that time when he formulated and published his theory on evolution of species. Both theology and the contemporary science (at that time) point towards an age of Earth (6000 years or 40 million years), which is absolutely not compatible with the concept of Evolution and with that age, there is not enough time for the Natural Selection to work. This backdrop of Earth’s age is very critical to understand Darwin’s thought process and his confidence in his theory.

Without even establishing anything and without even explaining the concept or the meaning of Natural Selection12, Hussain is trying to conclude that Charles Lyell’s 6th point (gradually accumulated changes create new species in time) is what Darwin’s Evolution theory is all about without explaining why there should be a change in the first place.

12 Origin of Species, Charles Darwin, Signet Classics, 150th, Anniversary Edition, Chapter 4, Page 76


The key part of Natural Selection is Why Natural Selection? Under what circumstances Natural Selection works. That’s exactly what Hussain should try to understand and explain if he thinks he is an expert in Darwin’s Evolution Theory. What N M Hussain expects in the Origin of Species theory is the answer to Earth’s 4.5 billion years of History well defined. Which means how each species formed and how it got evolved. He didn’t get the concept that Charles Darwin’s “On the Origin of Species” is a collection of theories (with examples) on what you see around in different geographic locations across the world and created a scientific model, which can give a scientific explanation on the diversity of species on planet Earth. Every theory requires empirical data to support the theories predictions. However, the key aspect is trying to figure what exactly the theory is trying to emphasize. Now lets look at Hussain’s conclusion on “On the Origin of Species”.

Here Hussain explains that, “On Origin of the Species” should contain details of atleast one species (from the beginning) from the current 2 million species in this world. This is the perfect example that he doesn’t understand Darwin’s theory. He needs to understand that, to explain that you need to go through 4.5 billion years of Earth’s history13 (check out the BBC site for the Prehistoric Life on Earth), and the most critical part of Darwin’s theory is Common Descent running into the last 3 billion years of Earth’s history. So, from the above paragraph (from Hussain) following things we can infer.

1. Hussain doesn’t understand that the Earth is 4.5 billion years old 2. Hussain doesn’t understand the concept of Common Descent. 3. Hussain doesn’t accept single origin of life. 4. Hussain doesn’t understand that Eukaryote14 evolved around 2.7 billions

years ago. 5. Hussain expects one book to reveal all the details of 3 billion years of species

history!

13 BBC – History of Life on Earth 14 Eukaryote -‐ Wikipedia


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1.1.2 Geological Time Periods (from BBC) Following data from BBC Site shows various geological time on Earth. It’s important to understand this history to get the complete grasp of Evolution.

Following extract is from BBC site on Prehistoric life of Earth15 The Earth is a little over 4.5 billion years old, its oldest materials being 4.3 billion-‐year-‐old zircon crystals. Its earliest times were geologically violent, and it suffered constant bombardment from meteorites. When this ended, the Earth cooled and its surface solidified to a crust -‐ the first solid rocks. There were no continents as yet, just a global ocean peppered with small islands. Erosion, sedimentation and volcanic activity -‐ possibly assisted by more meteor impacts -‐ eventually created small proto-‐continents which grew until they reached roughly their current size 2.5 billion years ago. The continents have since repeatedly collided and been torn apart, so maps of Earth in the distant past are quite different to today's.

The history of life on Earth began about 3.8 billion years ago, initially with single-‐celled prokaryotic cells, such as bacteria. Multicellular life evolved over a billion years later and it's only in the last 570 million years that the kind of life forms we are familiar with began to evolve, starting with arthropods, followed by fish 530 million years ago (Ma), land plants 475Ma and forests 385Ma. Mammals didn't evolve until 200Ma and our own species, Homo sapiens, only 200,000 years ago. So humans have been around for a mere 0.004% of the Earth's history.

1.1.3 Geological Time Line (from BBC)

15 BBC – Prehistoric Life of Earth


1.1.4 Tree of Life (from BBC)


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However, Hussain, as a creationist how can he accept Evolution, because his whole purpose is not to understand Evolution but to say God Created all species at the same time. His prejudiced mind is completely closed to Science. Hussain expects that “On Origin of the Species” can be worth its salt, only if it contains 4.5 billion years of Earth history. So, its very clear that Hussain, started his article with a prejudiced mind and trying to prove that Evolution is wrong without understanding what it really means and has no clue about Earth’s history. After going through the 4.5 billion years of Earth’s history, what will be the version of a creationist?

1. God Created Universe 2. God Created Earth 3. God Created Species 4. God Created Man

Can we ask any questions on the above four statements? Like the following:

1. How old is Universe? 2. How old is Sun? 3. How old is Earth? 4. Is the Universe static or expanding? 5. What will be the fate of the Universe? 6. Are all these diverse set of species got created at the same time? 7. What about the case of 99% of species got extinct? 8. If an asteroid didn’t hit Earth 60 million years ago, Dinosaurs will be still

ruling this planet! So, did God, purposefully destroyed Dinosaurs to create Humans?

9. What’s space and time? 10. Is Time absolute? 11. What’s primary matter or consciousness?

Science is all about answering the RIGHT questions and more. When you ask these questions, a creationist will hide behind religion and say, “that’s not the purpose of the religion!” Readers must be thinking now, why I am talking about Universe, Earth and Stars in an article about Evolution. Evolution is there everywhere, there is a cosmic Evolution (formation of Stars and planets) and there is biological Evolution. Understanding the history and geological time period is critical to understand Evolution and Darwin’s vision. Now where is science when Hussain’s belief says that God created every species? That’s nothing but faith. That’s where his confusion starts, confusing faith with Science. You don’t need to bring in Science if you want be spiritual. Religion and


Science has two very distinctive roles. It’s ok to be spiritual, and the golden rule to follow, never mix up your personal spiritual beliefs with Science! As Hussain is confused about Earth’s history and the theories of Evolution, lets move forward and look how Hussain presented the case even after it’s very clear about his intentions. In the next section Hussain describes Darwin’s example and he is concluding that, it never happens in nature and its nothing but Darwin’s pure imagination. Without even explaining the theory and the accompanying facts, without even evaluating the facts, he declared that Evolution Theory doesn’t work. Now lets see what Darwin says in Origin of Species about his examples to illustrate the concept of Natural Selection. “I must beg permission to give one or two imaginary illustrations16.” -‐ Charles Darwin, Chapter IV, On the Origin of the Species, Page 86

When Darwin took the readers permission to explain the concept of Natural Selection using an imaginary illustration, Hussain portrayed as his own conclusion! I could understand if this article is published in 1859. However after 150 years there are ‘n’ numbers of evidence available in Genetics and Organism level to support Darwin’s Theory. The third section of this article focuses on few prime examples to illustrate micro and macroevolution as well as it will discuss the concept of design or bad design in animals. His paragraph ends with the statement that Darwin never gave any evidence for his theory. Science illiterates will be so happy to read Hussain’s statement as Hussain is exploiting their ignorance. How intelligent to confuse the normal readers!

16 On Origin of Species, Charles Darwin, Signet Classics 150th Anniversary Edition


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This kind of tactics is called FUD Factor; inject Fear, Uncertainty and Doubt in other people’s mind. This is what priests did to the common man for the past 5 thousand years. Let us look at how theoretical physics works. Take Einstein’s Relativity17 Theory or Newton’s Laws of Gravity18, these theories had the predictive power.

• Once the observations where applied to the hypothesis, it produced accurate results.

• This is verified by ‘n’ number of scientists across the world. That’s when it became a theory.

• In Newton’s Laws of Gravity it predicted everything except Mercury’s path (around Sun), because observation and path produced by Newton’s Law of Gravity were not matching (slight variations). This got fixed with Einstein’s General Theory of Relativity. Today to send a Rocket to space you need only Newton’s Law. However, if the payload of the rocket contains a GPS satellite then you need Einstein’s Special theory of Relativity and General Theory of Relativity, without these theories, the discrepancies in finding your location will be around 11 kms per day.

That’s the kind of predictive power in Darwin’s theory detailed in “On Origin of the Species” book. It had the predictive power to predict the evolution of species from microbes to macro organisms. Now lets look at what exactly is “On the Origin of Species” is all about. Before that lets review the fundamental creationist view on Origin of Species. God created all species as is and everything required to support them. Can you prove this? No, its nothing but you have to believe and that’s called faith and not Science. It’s pointless to get into a Science Vs. Religion debate. I feel it’s not a debatable subject because of its distinctive nature and goals.

Like I said before it’s OK to believe in God and have faith, that doesn’t mean, that’s how Science should work. Faith is subjective and it’s very personal. Science is Objective and is a continuous iterative process. Iteration refines the scientific facts with more knowledge, data and understanding of the universe and nature. So, the purpose of this article is not to establish the existence of God or deny it, but to review the claims made by Hussain against Evolution, and analyze those claims. In the next section we will examine the key concepts in the “On the Origin of the Species” which Hussain failed to elaborate in his article. Then we will compare the alternate theories on Evolution like Creationism and Intelligent Design. The reason

17 Einstein’s General Theory of Relativity – Wikipedia 18 Newton’s Law of Gravity – Wikipedia


for this comparison is to give the reader a holistic picture on this topic, so that they can make their own judgments on what to believe and what not to believe. So, lets get started with Darwin’s theory of Evolution.


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1.2 Understanding Darwin’s Theory of Evolution With this backdrop let us look into what’s Darwin’s “On Origin of Species” first published in 1859, (153 years ago) is all about. Darwin had an extra ordinary vision on the Evolution of Species and came up with two brilliant and spectacular ideas and the third one (2.1) is an inference from his second idea.

1.2.1 Idea 1 – Natural Selection19 “Can it, then, be thought improbable … that other variations useful in some way to each being in the great and complex battle of life, should sometimes occur in the course of thousands of generations? If such do occur, can we doubt (remembering that many more individuals are born than can possibly survive) that individuals having advantage, however slight, over others, would have the best chance of surviving and of procreating their kind? On the other hand, we may feel sure that any variation in the least degree injurious would be rigidly destroyed. This preservation of favorable variations and the rejection of injurious variations I call Natural Selection” – Chapter IV, “Natural Selection” On the Origin of Species, Page 77 Then comes the extra ordinary vision of Darwin, which says this process would connect all life’s form via their descent from common ancestors.

1.2.2 Idea 2 – Common Descent20 (Descent with Modification) Several classes of facts… seem to me to proclaim so plainly, that the innumerable species, genera, and families of organic beings, with which this world is peopled, have all descended, each within its own class or group, from common parents, and have all been modified in the course of descent. – Chapter XIV, “Mutual Affinities of Organic Beings: Morphology: Embryology:” On the Origin of Species, Page 477 Then the astounding claim

1.2.3 Idea 2.1 – Single Origin of Life21 Therefore I should infer from analogy that probably all the organic beings, which have ever lived on this earth, have descended from on primordial form, into which life was first breathed. – Chapter XV, “Recapitulations and Conclusions:” On the Origin of Species, Page 502

1.2.4 Idea 3 – Variation in Rate of Change22 Species of different genera and classes have not changed at the same rate, or in the same degree.

19 On Origin of Species, Charles Darwin, Signet Classics 150th Anniversary Edition, Chapter 4, Page 77 20 On Origin of Species, Charles Darwin, Signet Classics 150th Anniversary Edition, Chapter 14, Page 477 21 On Origin of Species, Charles Darwin, Signet Classics 150th Anniversary Edition, Chapter 15, Page 502 22 On Origin of Species, Charles Darwin, Signet Classics 150th Anniversary Edition, Chapter 11, Page 345


-‐ Charles Darwin, Chapter XI “On the Geological succession of Organic Beings” On the Origin of Species, Page 345

In the fifth edition Darwin wrote “Many species when once formed never undergo any further change but become extinct without leaving modified descendants; and the periods during which species have undergone modifications, though long as measure by years have probably been short in comparison with the periods during which they have retained the same form.” -‐ Charles Darwin23, Chapter XV “Recapitulation and Conclusion”, On the Origin of Species, Page 483

1.2.5 Natural Selection So, from the above ideas from “On the Origin of the Species” what are the key ingredients to fuel the Evolution? Let us summarize key elements from Idea 1 – “Natural Selection” (check the words highlighted in red).

1. Variation 2. Selection (advantage) 3. Time (thousands of generations)

Understanding this powerful concept is key for the Evolution theory. There is huge amount of evidences confirming Natural Selection. Understanding the reasons behind Natural Selection is the key to your understanding of origin of species. Environmental factors play a key role in Natural Selection along with time. At the genetic level, mutation plays the most critical role and understanding the genotype, which describes the traits in the organism, and the phenotype, which makes the trait visible. We will revisit Natural Selection after getting a brief idea on DNA and mutations. The next key aspect of Darwin’s theory is the Descent with Modifications. Here the concept is not for single organism. It’s for the entire group of species in a particular environment and descent with modifications traces back to a single origin of life as per Darwin. “DNA sequencing has confirmed beyond any doubt that all living creatures share a common origin. Innumerable examples of evolution in action can be seen all around us, from the pollution-‐matching peppered moth to fast-‐changing viruses such as HIV and H5N1 bird flu. Evolution is as firmly established a scientific fact as the roundness of the Earth.” (Quote from New Scientist24)

23 On Origin of Species, Charles Darwin, Signet Classics 150th Anniversary Edition, Chapter 15, Page 483 24 New Scientist -‐ http://www.newscientist.com/article/dn13620-‐evolution-‐24-‐myths-‐and-‐misconceptions.html


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The crystal clear evidence comes in Genetic Science. The most interesting case is the 100,000 years fight between Homo sapiens and Malaria. The most devastating news on malaria in the recent times is, it is going to be incurable disease soon, because malaria is evolving pretty fast. Malaria already accounts for millions of deaths every year! In modern Science Evolution happens at two levels

1. Micro Evolution through Natural Selection 2. Macro Evolution through Natural Selection

To understand Micro Evolution, we will look into the structure of DNA and mutations in sections 1.3 Understanding Genome and 1.4. Mutations. For Macroevolution, we will look at the evidence presented in this article. In both levels there is a huge amount of evidence supporting Darwin’s Natural Selection. Before we jump into the next sections on Science, let us try to analyze the creationist’s views on Natural Selection.

1.2.6 Refuting Creationist claim that Natural Selection Doesn’t Work Let us look at Hussain’s perspective from his article.

Now here he is concluding that the Origin of Species can’t be explained by Natural Selection and then making critical statement that Natural Selection doesn’t have that capability. To come back to his statement that Natural Selection can’t explain evolution is absolutely wrong. If his analysis is logical and scientific, he must explain why Natural Selection won’t work and what’s the alternative scientific theory if there are any.


Here are the reasons why his conclusions are wrong

1. The creationist never tried to explain what Natural Selection is all about and refused to give an explanation instead just proclaimed his opinion that Natural Selection doesn’t work instead of giving any logical arguments. His statement is poorly out of ignorance and his complete blindness to modern science. Its very clear that Hussain has no clue about Natural Selection.

2. To refute Hussain’s claim that Natural Selection doesn’t work, the best example is the case I mentioned under Microevolution in Genetic Science, the 100,000 years fight between Homo sapiens and Malaria (more details under evidence section). If he understood the concept of Natural Selection and researched on that, he would have found 1000s and 1000s of evidences from different wings of evolutionary biology. I have created a separate section for evidences highlighting some of the prominent evidences on Evolution.

3. Hussain has no clue about the age of Earth and has no answers on why different species appeared in different (as per the evolution theory) geological time. Without Natural Selection it’s impossible for species to appear the way fossil records points out.

4. Today, evidence for natural selection you will find in genetic science (DNA, genes), fossil records, morphology analysis etc. The evidence section clearly establishes this case. They are books and videos (available in the Explore section) from top universities explaining how Natural Selection works at the genetic level.

Before we get deep into a critical review of Hussain’s article its important to understand his target audience. The nature of Hussain’s article reveals very clearly his target audience and his intentions and it will be very interesting to understand the Hussain’s target audience. It definitely can’t be educated scientifically literate community. Imagine this is the cover story of a magazine (I don’t know how popular that magazine is). So, with the initial few pages I get a feeling that the Hussain’s article is targeted at scientifically illiterate segment who heard about evolution but is in a confused state whether to accept that or not, and always in a continuous conflict with their religious beliefs which is creationism. When their kids go to school and learn about evolution they are not sure what their kids learning is right or wrong.


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1.2.7 Misconceptions about Evolution Theory25 Misconception: Evolution is a theory about Origin of Life Correction: Evolution is theory focuses on the Origin of Species. It’s about how life diversified and branched out. So it’s not about Origin of Life. Misconception: Evolution is by Chance Correction: Evolution is NOT by chance, mutation is random but Natural Selection is NOT random. Misconception: Individual organisms can evolve (into new species) during a single lifespan. Correction: Evolutionary change is based on changes in the genetic makeup of the population over time and Population, and not individual organisms, evolve. Misconception: Evolution only occurs slowly and gradually Correction: Evolution occurs slowly and gradually, but it can also occur rapidly, and the rate of change can be different from species to species. Misconception: Evolution results in organisms always getting better and better. Correction: Natural Selection does result in improved abilities to survive and reproduce. Natural Selection allows the survival of the individuals with a range of traits, individuals that are good enough to survive. There are other mechanisms of evolution that don't cause adaptive change. Mutation, migration, and genetic drift may cause populations to evolve in ways that are actually harmful overall or make them less suitable for their environments. Evolution doesn’t make the organism better, it makes it fittest for the current environment. Misconception: Genetic mutation arise in response to the environment Correction: Mutations are constantly occurring, depends upon the environment the mutation can be good, bad or neutral. Natural selection picks up the mutation, which is beneficial for the current crisis the species is facing. Even if that mutation solves the current crisis, it may be potentially harmful in the future. Which shows that Natural Selection doesn’t do long term planning something a designer keeps in mind when the designer designs something. The classic example is the Sickle Cell mutation to combat malaria by the Humans. However, we know that inheriting sickle cell from both parents is fatal.

25 Misconceptions about Evolution – Berkeley University


1.2.8 Predictive Power of Evolution Here is an example of how Evolution Theory predicts where to find a specific fossil. Evolution tells us

1. The time species lived, helps to narrow down the rock formation to look for fossils.

2. About the habitat of the species. 3. Species morphology26, which includes species outward appearance (shape,

structure, color, pattern) and the internal structures like organs and bones. This doesn’t mean that it’s a like a GPS location, so that the only thing the paleontologist27 needs to do is go and dig up the fossil. An example is the discovery of the Tiktaalik28 fossil, which is a transition fossil between fish and Tetrapods29, the first four legged vertebrates and their descendants including the amphibians, reptiles, birds and mammals. In 2004, a field crew digging in the Canadian Arctic (their fourth trip to Artic in summer) unearthed the fossil remains of a half-‐fish, half-‐amphibian that would all but confirm paleontologists' theories about how land-‐dwelling Tetrapods (four-‐limbed animals, including us) evolved from their fish ancestors. The animal was a so-‐called lobe-‐finned fish that lived about 375 million years ago. Named Tiktaalik rosae by its discoverers, it is a classic example of a transitional form, one that bridges the evolutionary gap between two quite different types of animal. Read more in PBS (Nova) web site under Fossil evidence30.

In the next section we will get more in depth understanding of DNA and Mutations and how Natural Selection works at Microevolution.

26 Morphology – Wikipedia 27 Paleontology -‐ Wikipedia 28 Tiktaalik Transition between Fish and Tetrapods – Wikipedia 29 Tetrapod -‐ Wikipedia 30 PBS Nova Transition Fossil Evidence


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1.3 Understanding Genome – DNA, Chromosomes, Genes & Alleles The entire DNA sequence is called Genome and in humans it’s around 3.4 billion base pairs. In computer storage terms it will take 3 Gigabytes of storage to store the human genome of 3.2 billion bases.

1.3.1 DNA31 DeoxyriboNucleic Acid in short DNA is the hereditary material in humans and almost all organisms. Most DNA is located in the Cell Nucleus. However a small amount of DNA can also be found in the mitochondria, which is the powerhouse of a cell. This DNA is known as mitochondrial DNA or mtDNA. The DNA is composed of four chemical bases:

• Adenine (A) • Guanine (G) • Cytosine (C) • Thymine (T)

Human DNA consists of 3 billion bases and more than 99% of those bases are the same in all the people.

Figure 1: Double Helix structure with base pairs, sugar molecule and phosphate molecule.

The four chemical bases join based on special rules32. A always pairs with T and C always pairs with G. Double Helix The chemical bases (ATCG), pair up with each other to form double helix (figure 1). Each base is attached to eh sugar molecule and phosphate molecule and all the three put together (Base pairs, Sugar molecule, phosphate molecule) is called a nucleotide. The Nucleotides are arranged in two long strands that form a spiral called a double helix. DNA molecules are informational molecules encoding the genetic instructions used in the development and functioning of all known living organisms and may viruses. 31 DNA – Wikipedia: http://en.wikipedia.org/wiki/DNA 32 University of Utah -‐ http://learn.genetics.utah.edu/content/begin/tour/


The DNA Grammar33 The DNA code uses groups of three 'letters' to make meaning. This means that when the cell reads the instructions encoded in the DNA sequence to make a protein, it reads it three letters at a time. Most groups of three letters -‐ known as triplets or codons -‐ code for an amino acid. Since there are four different DNA letters (A, G, C and T), there are 43 = 4 x 4 x 4 = 64 different combinations that can be used. However, as there are only 20 different types of amino acid, some of these 64 codons code for the same amino acid. Some of the 64 codons don't code for any of the amino acids. Instead they provide the punctuation and grammar, like where the cell should start and stop

Preliminary evidence34 indicating that the genetic code was indeed a triplet code came from an experiment by Francis Crick and Sydney Brenner (1961). This experiment examined the effect of frameshift mutations on protein synthesis. Frameshift mutations35 are much more disruptive to the genetic code than simple base substitutions, because they involve a base insertion or deletion, thus changing the number of bases and their positions in a gene. For example, the mutagen proflavine causes frameshift mutations by inserting itself between DNA bases. The presence of proflavine in a DNA molecule thus interferes with the molecule's replication such that the resultant DNA copy has a base inserted or deleted.

33 http://www.yourgenome.org/dgg/general/proteins/proteins_1.shtml 34 Nature: Nucleic Acids to Amino Acids: DNA Species proteins 35 Nature: Genetic Mutations


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1.3.2 Mitochondrial DNA36 Mitochondrial DNA has a special role in evolutionary science as its inherited only through the mother. Compare to the DNA in the nucleus, mitochondrial DNA doesn’t have to go through lot of changes. Mitochondrial DNA contains 37 genes, all of which are essential for normal mitochondrial function.

Mitochondrial DNA has a circular shape compare to the Double Helix of the DNA in the nucleus of the cell.

36 University of Utah -‐ http://learn.genetics.utah.edu/content/extras/molgen/four_types.html


1.3.3 Chromosome37 In the nucleus of each cell, the DNA molecule is packaged into thread-‐like structures called chromosomes. Each chromosome is made up of DNA tightly coiled many times around proteins called histones that support its structure. Chromosomes are made up of genes. Each chromosome has a constriction point called the centromere, which divides the chromosome into two sections, or “arms.” The short arm of the chromosome is labeled the “p arm.” The long arm of the chromosome is labeled the “q arm.” The location of the centromere on each chromosome gives the chromosome its characteristic shape, and can be used to help describe the location of specific genes. Chromosomes38 come in pairs (as shown in the figure below). Each chromosome is a tightly packed strand of DNA. There are two strands of DNA joined together at the centromere to form an X shaped structure. One strand comes from mother and one from father. Because there are two strands of DNA, it means that animals have two copies of every gene, rather one copy as with E. Coli (bacteria). The sperm and egg from the mother and father each contribute one copy of each chromosome. To form the single strand in the sperm or egg, one or the other copy of gene is randomly chosen. Because of the random nature of gene selection, each child gets a different mix of genes from the DNA of the mother and father.

In humans, each cell normally contains 23 pairs of chromosomes, for a total of 46. Twenty-‐two of these pairs, called autosomes, look the same in both males and 37 http://ghr.nlm.nih.gov/handbook/basics/howmanychromosomes 38 http://science.howstuffworks.com/environmental/life/genetic/gene-‐pool1.htm


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females. The 23rd pair, the sex chromosomes, differ between males and females. Females have two copies of the X chromosome, while males have one X and one Y chromosome. Chromosome 2 is an interesting candidate in evolution. The reason for that is Apes has 24 pair of chromosomes, that’s a total of 48. So, if we are evolved from a common ancestor then how come we got only 23 pair of chromosomes? You will find the answer in “evidence section”.

1.3.4 Gene39

A gene is the basic physical and functional unit of heredity. Genes, which are made up of DNA, act as instructions to make molecules called proteins. In humans, genes vary in size from a few hundred DNA bases to more than 2 million bases. The Human Genome Project has estimated that humans have between 20,000 and 25,000 genes.

Every person has two copies of each gene, one inherited from each parent. Most genes are the same in all people, but a small number of genes (less than 1 percent of the total) are slightly different between people.

A gene40 is nothing but a template for creating a protein. This means that, in any plant or animal, there are actually two templates for every protein. In some cases, the two templates are the same (homozygous), while in some other cases the templates are different (heterozygous). Each gene appears at a certain location on a certain chromosome, and the location of a particular gene is called locus of the gene.

39 http://ghr.nlm.nih.gov/handbook/basics/gene 40 http://science.howstuffworks.com/environmental/life/genetic/gene-‐pool1.htm


1.3.5 Allele

Alleles are forms of the same gene with small differences in their sequence of DNA bases. These small differences contribute to each person’s unique physical features.

1.3.6 Control Genes41 Control genes are like master keys to a set of locks. It controls other genes, determining when and where other genes are turned on. Mutations in these parts of genome can substantially change the way organism is built. Mutation on a single gene is similar to a bad note produced by a specific music player. However if the mutation happens to the conductor of an orchestra, then the result will be fatal. Many organisms have powerful control genes that determine how the body is laid out. Some control genes are common to many organisms and are inherited from our common ancestor.

Hox Genes Hox42 genes help layout the basic body forms of many animals including humans, flies, and worms. The instructions are carried out as embryo develops.

41 Berkeley University – Control Genes 42 Berkeley University – Hox Gene


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Many creationists show that the mutations in control genes as an example of “mutations are always bad” concept. It can bring in only fatal changes to an organism. Their objectives are very simple – introduce fear in the young mind, so that they are away from science. Mutations to control genes can transform one body part into another. Scientists have studied flies carrying Hox gene mutations that sprout leg on their foreheads instead of antennae! You will find this picture in a creationists article proclaiming that mutations are bad! They will never enlighten the readers that it’s in the control gene.

PAX643 Gene PAX6 gene is a member of the Pax Gene Family. It acts as a master control gene for the development of eyes and other sensory organs. Mouse PAX6 gen can trigger eye development in Drosophila melanogaster (Fruit Fly), and mouse and human PAX6 have identical Amino acid sequences.

1.3.7 Gene Pool44 The combination of all the versions of all the genes in in a species is called the gene pool of the species. Some of the arguments creationists propose is because of the gene pool, a species cant change over to completely different species over a period of time. Here their argument is based on the assumption that variations has a limitations and for them time is nothing but few years. Along with the same argument they say Mutations are always harmful. If you take these two arguments then what you realize is all the species will die out because of harmful mutations over a period of time because of the restrictive gene pool. In the next section we will see how mutations work and the various models with which mutations work.

43 Gehring WJ, Ikeo K (September 1999). "Pax 6: mastering eye morphogenesis and eye evolution". Trends Genet. 15 (9): 371–7 44 Gene Pool -‐ http://science.howstuffworks.com/environmental/life/genetic/gene-‐pool2.htm


1.3.8 Comparing45 Genotype and Phenotype Genotype is the specific genetic code that provides information for a particular trait in the organism. While the phenotype is the visible expressed trait, such as eye color, hair color etc. The phenotype depends upon the genotype but also can be influenced by environmental factors. An organism's genotype is a major (the largest by far for morphology) influencing factor in the development of its phenotype, but it is not the only one. Even two organisms with identical genotypes normally differ in their phenotypes.

Genotype Phenotype Refers to: The information contained on

two alleles in the cell. An expressed and observable trait, e.g. hair color.

Can be determined by:

Genotyping – using a biological assay, such as PCR, to find out what genes are on an allele.

Observation of the individual.

Depends upon: The hereditary information that was given to an individual by their parents.

Genotype and the influence of the environment.

Contains: All the hereditary information of an individual, even if those genes are not expressed.

Expressed genes only.

Inheritance: Partly inherited by offspring, as one of the two alleles is passed on during reproduction.

Cannot be inherited.

It is the organism's physical properties, which directly determine its chances of survival and reproductive output, while the inheritance of physical properties occurs only as a secondary consequence of the inheritance of genes. Therefore, to properly understand the theory of evolution via natural selection, one must understand the genotype–phenotype46 distinction.

45 http://www.diffen.com/difference/Genotype_vs_Phenotype 46 Wikipedia -‐ http://en.wikipedia.org/wiki/Genotype-‐phenotype_distinction


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1.3.9 Amino Acids So, finally we are into chemistry now.


1.4 Mutation47 Following section is from Nature (magazine) Education section. DNA is a dynamic and adaptable molecule. As such, the nucleotide sequences found within it are subject to change as the result of a phenomenon called mutation. Depending on how a particular mutation modifies an organism's genetic makeup, it can prove harmless, helpful, or even hurtful. Sometimes, a mutation may even cause dramatic changes in the physiology of an affected organism. Of course, in order to better understand the varying effects of mutations, it is first necessary to understand what mutations are and how they occur. The DNA in any cell can be altered through environmental exposure to certain chemicals, ultraviolet radiation, other genetic insults, or even errors that occur during the process of replication. If a mutation occurs in a germ-‐line cell (one that will give rise to gametes, i.e., egg or sperm cells), then this mutation can be passed to an organism's offspring. This means that every cell in the developing embryo will carry the mutation. As opposed to germ-‐line mutations, somatic mutations occur in cells found elsewhere in an organism's body. Such mutations are passed to daughter cells during the process of mitosis (Figure 0), but they are not passed to offspring conceived via sexual reproduction.

Figure 0: The two basic classes of mutations are somatic mutations and germ-‐line mutations. Mutations are random changes in the sequence of the DNA in a gene. Mutations can be grouped into two main categories based on where they occur: somatic mutations and germ-‐line mutations

1.4.1 Where do mutations occur?

Somatic mutations take place in non-‐reproductive cells. Many kinds of somatic mutations have no obvious effect on an organism, because genetically normal body cells are able to compensate for the mutated cells.

47 Nature – DNA is constantly changing through the Process of Mutation


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Nonetheless, certain other mutations can greatly impact the life and function of an organism. For example, somatic mutations that affect cell division (particularly those that allow cells to divide uncontrollably) are the basis for many forms of cancer. Germ-‐line mutations occur in gametes or in cells that eventually produce gametes. In contrast with somatic mutations, germ-‐line mutations are passed on to an organism's progeny. As a result, future generations of organisms will carry the mutation in all of their cells (both somatic and germ-‐line).

1.4.2 Kinds of Mutation There are two kinds of Mutations Gene Level and Chromosome level mutations. Mutations aren't just grouped according to where they occur frequently, the length of the nucleotide sequences they affect also categorizes them. Gene-‐Level Mutations – Changes to short stretches of nucleotides are called gene-‐level mutations, because these mutations affect the specific genes that provide instructions for various functional molecules, including proteins. Changes in these molecules can have an impact on any number of an organism's physical characteristics. Chromosomal Mutations -‐ As opposed to gene-‐level mutations, mutations that alter longer stretches of DNA (ranging from multiple genes up to entire chromosomes) are called chromosomal mutations. These mutations often have serious consequences for affected organisms. Because gene-‐level mutations are more common than chromosomal mutations, the following sections focus on these smaller alterations to the normal genetic sequence.

1.4.3 Mutation Models48 There are four models

1. Base Substitution 2. Insertion 3. Deletion 4. Frameshift

Base Substitution Base substitutions are the simplest type of gene-‐level mutation, and they involve the swapping of one nucleotide for another during DNA replication. For example, during replication, a thymine nucleotide might be inserted in place of a guanine nucleotide. 48 Nature – DNA is constantly changing through the Process of Mutation


With base substitution mutations, only a single nucleotide within a gene sequence is changed, so only one codon is affected (Figure 1).

Figure 1: Only a single codon in the gene sequence is changed in base substitution mutation. Although a base substitution alters only a single codon in a gene, it can still have a significant impact on protein production. In fact, depending on the nature of the codon change, base substitutions can lead to three different subcategories of mutations. The first of these subcategories consists of missense mutations, in which the altered codon leads to insertion of an incorrect amino acid into a protein molecule during translation; the second consists of nonsense mutations, in which the altered codon prematurely terminates synthesis of a protein molecule; and the third consists of silent mutations, in which the altered codon codes for the same amino acid as the unaltered codon. Insertion Insertions and deletions are two other types of mutations that can affect cells at the gene level. An insertion mutation occurs when an extra nucleotide is added to the DNA strand during replication. This can happen when the replicating strand "slips," or wrinkles, which allows the extra nucleotide to be incorporated (Figure 2). Strand slippage can also lead to deletion mutations.

Figure 2: During an insertion mutation, the replicating strand "slips" or forms a wrinkle, which causes the extra nucleotide to be incorporated.


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Deletion A deletion mutation occurs when a wrinkle forms on the DNA template strand and subsequently causes a nucleotide to be omitted from the replicated strand (Figure 3).

Figure 3: In a deletion mutation, a wrinkle forms on the DNA template strand, which causes a nucleotide to be omitted from the replicated strand.

Frameshift49 Insertion or deletion of one or more nucleotides during replication can also lead to another type of mutation known as a frameshift mutation. The outcome of a frameshift mutation is complete alteration of the amino acid sequence of a protein. This alteration occurs during translation because ribosomes read the mRNA strand in terms of codons, or groups of three nucleotides. These groups are called the reading frame. Thus, if the number of bases removed from or inserted into a segment of DNA is not a multiple of three (Figure 4a), the reading frame transcribed to the mRNA will be completely changed (Figure 4b). Consequently, once it encounters the mutation, the ribosome will read the mRNA sequence differently, which can result in the production of an entirely different sequence of amino acids in the growing polypeptide chain. To better understand frameshift mutations, let's consider the analogy of words as codons, and letters within those words as nucleotides. Each word itself has a separate meaning, as each codons represents one amino acid. The following sentence is composed entirely of three-‐letter words, each

Figure 4: If the number of bases removed or inserted from a segment of DNA is not a multiple of three (a), a different sequence with a different set of reading

49 Nature – DNA is constantly changing through the Process of Mutation


representing a three-‐letter codon: frames is transcribed to mRNA (b).

THE BIG BAD FLY HAD ONE RED EYE AND ONE BLU EYE.

Now, suppose that a mutation eliminates the sixth nucleotide, in this case the letter "G". This deletion means that the letters shift, and the rest of the sentence contains entirely new "words":

THE BIB ADF LYH ADO NER EDE YEA NDO NEB LUE YE.

This error changes the relationship of all nucleotides to each codon, and effectively changes every single codon in the sequence. Consequently, there is a widespread change in the amino acid sequence of the protein. Lets consider an example with an RNA sequence that codes for a sequence of amino acids:

AUG AAA CUU CGC AGG AUG AUG AUG

With the triplet code, the sequence shown in figure 5 corresponds to a protein made of the following amino acids: Methionine-‐Lysine-‐Leucine-‐Arginine-‐Arginine-‐Methionine-‐Methionine-‐Methionine

Figure 5: This sequence of mRNA codes for the amino acids methionine-lysine-leucine-arginine-arginine-methionine-methionine-methionine. Now, suppose that a mutation occurs during replication, and it results in deletion of the fourth nucleotide in the sequence. When separated into triplet codons, the nucleotide sequence would now read as follows (Figure 6): AUG AAC UUC GCA GGA UGA UGA UG This series of codons would encode the following sequence of amino acids: Methionine-‐Asparagine-‐Phenylalanine-‐Alanine-‐Glycine-‐STOP-‐STOP


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Figure 6: If the fourth nucleotide in the sequence is deleted, the reading frame shifts and the amino acid sequence changes to methionine-asparagine-phenylalanine-alanine-glycine-STOP-STOP Each of the stop codons tells the ribosome to terminate protein synthesis at that point. Consequently, the mutant protein is entirely different due to the deletion of the fourth nucleotide, and it is also shorter due to the appearance of a premature stop codon. This mutant protein will be unable to perform its necessary function in the cell.

1.4.4 Types of DNA Mutations and Their Impact50 Class of Mutation

Type of Mutation

Description

Human Disease(s) Linked to This Mutation

Point mutation

Substitution

One base is incorrectly added during replication and replaces the pair in the corresponding position on the complementary strand

Sickle-cell anemia

Insertion

One or more extra nucleotides are inserted into replicating DNA, often resulting in a frameshift

One form of beta-thalassemia

Deletion

One or more nucleotides is "skipped" during replication or otherwise excised, often resulting in a frameshift

Cystic fibrosis

Chromosomal mutation

Inversion

One region of a chromosome is flipped and reinserted

Opitz-Kaveggia syndrome

Deletion

A region of a chromosome is lost, resulting in the absence of all the genes in that area

Cri du chat syndrome

Duplication

A region of a chromosome is repeated, resulting in an increase in dosage from the genes in that region

Some cancers

Translocation

A region from one chromosome is aberrantly attached to another chromosome

One form of leukemia

Copy number variation

Gene amplification

The number of tandem copies of a locus is increased

Some breast cancers

Expanding trinucleotide repeat

The normal number of repeated trinucleotide sequences is expanded

Fragile X syndrome, Huntington's disease

50 Nature – Genetic Mutations and their Impact


1.4.5 What causes mutations?51 Mutations can arise in cells of all types as a result of a variety of factors, including chance. In fact, some of the mutations discussed above are the result of spontaneous events during replication, and they are thus known as spontaneous mutations. Slippage of the DNA template strand and subsequent insertion of an extra nucleotide is one example of a spontaneous mutation; excess flexibility of the DNA strand and the subsequent mispairing of bases is another. Environmental exposure to certain chemicals, ultraviolet radiation, or other external factors can also cause DNA to change. These external agents of genetic change are called mutagens. Exposure to mutagens often causes alterations in the molecular structure of nucleotides, ultimately causing substitutions, insertions, and deletions in the DNA sequence.

1.4.6 What are the consequences of mutations?52 Mutations are a source of genetic diversity in populations, and, as mentioned previously, they can have widely varying individual effects. In some cases, mutations prove beneficial to an organism by making it better able to adapt to environmental factors. In other situations, mutations are harmful to an organism — for instance, they might lead to increased susceptibility to illness or disease. In still other circumstances, mutations are neutral, proving neither beneficial nor detrimental outcomes to an organism. Thus, it is safe to say that the ultimate effects of mutations are as widely varied as the types of mutations themselves. We have gone through a brief tour on DNA and Mutations, now its time to take a relook at Natural Selection at the Genetic Level.

51 Nature – DNA is constantly changing through the Process of Mutation 52 Nature – DNA is constantly changing through the Process of Mutation


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1.5 Natural Selection at Genetic Level After the brief tour on DNA and Mutations, its time for us to take a relook at Natural Selection at the micro level – Genetics. There are two types of Natural Selection, to select the variants at the DNA level. These two models come out from Neutral Theory of Molecular Evolution.

• Positive Natural Selection • Negative Natural Selection

1.5.1 Neutral Theory: The Null Hypothesis of Molecular Evolution53 In the decades since its introduction, the neutral theory of evolution has become central to the study of evolution at the molecular level, in part because it provides a way to make strong predictions that can be tested against actual data. The neutral theory holds that most variation at the molecular level does not affect fitness and, therefore, stochastic processes best explain the evolutionary fate of genetic variation. This theory also presents a framework for ongoing exploration of two areas of research: biased gene conversion, and the impact of effective population size on the effective neutrality of genetic variants. In 1968, Motoo Kimura proposed a new hypothesis, now known as the neutral theory of molecular evolution (Kimura, 1968), Kimura subsequently summarized his theory as follows: "This neutral theory claims that the overwhelming majority of evolutionary changes at the molecular level are not caused by selection acting on advantageous mutants, but by random fixation of selectively neutral or very nearly neutral mutants through the cumulative effect of sampling drift (due to finite population number) under continued input of new mutations" (Kimura, 1991) It must be stressed that the neutral theory of molecular evolution is not an anti-‐Darwinian theory. Both the selectionist and neutral theories recognize that natural selection is responsible for the adaptation of organisms to their environment. Both also recognize that most new mutations in functionally important regions are deleterious and that purifying selection quickly removes these deleterious mutations from populations. Thus, these mutations do not contribute—or contribute very little—to sequence divergence between species and to polymorphisms within species. Rather, the dispute between selectionists and neutralists relates only to the relative proportion of neutral and advantageous mutations that contribute to sequence divergence and polymorphism. Analysis of genomic sequence data reveals that there is no "all or nothing" answer to this dispute. In fact, the proportion of neutral substitutions varies widely among

53 By Laurent Duret, Laboratory of Biometric and Evolutionary Biology, University of Claude Bernard, France, 2008 © Nature http://www.nature.com/scitable/topicpage/neutral-‐theory-‐the-‐null-‐hypothesis-‐of-‐molecular-‐839


taxa. However, it is now clearly established that non-‐adaptive processes cannot be neglected. Even in taxa in which selection is very effective, a large fraction of substitutions are indeed neutral. The classification of mutations into three distinct types—deleterious, neutral, and advantageous—is of course an oversimplification. In reality, there is a continuum from highly deleterious to weakly deleterious, nearly neutral, neutral, weakly advantageous, and strongly advantageous mutations Empirical data are consistent with this prediction. For example, in Drosophila species (where Ne is about 106), the proportion of non-‐synonymous substitutions that have been fixed by positive selection is about 50%. Contrast this with the data for hominids (with Ne around 10,000 to 30,000), where this proportion is close to zero. Similarly, the proportion of non-‐synonymous mutations that are effectively neutral is less than 16% in Drosophila, whereas it is about 30% in hominids (Eyre-‐Walker & Keightley, 2007).

1.5.2 Positive Natural Selection54 Positive natural selection, or the tendency of beneficial traits to increase in prevalence (frequency) in a population, is the driving force behind adaptive evolution. For a trait to undergo positive selection, it must have two characteristics. First, the trait must be beneficial; in other words, it must increase the organism's probability of surviving and reproducing. Second, the trait must be heritable so that it can be passed to an organism's offspring. Beneficial traits are extremely varied and may include anything from protective coloration, to the ability to utilize a new food source, to a change in size or shape that might be useful in a particular environment. If a trait results in more offspring who share the trait, then that trait is more likely to become common in the population than a trait that arises randomly. At the molecular level, selection occurs when a particular DNA variant becomes more common because of its effect on the organisms that carry it.

54 Nature -‐ http://www.nature.com/scitable/topicpage/Evolutionary-‐Adaptation-‐in-‐the-‐Human-‐Lineage-‐12397 By Stephen F Schaffner (MIT, Harvard, Cambridge USA), Pardis C Sabeti (Harvard, Cambridge) Evolutionary Adaption in the Human Lineage, © Nature


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1.5.3 Negative Natural Selection55 Selection is a powerful force in evolution, and it works in many ways. In the end, however, selection constantly sorts through the variation that is produced by mutations to select the fit and remove the unfit, while ignoring neutral changes. A few distinct types of selection are illustrated in Figure 1. • Stabilizing selection keeps the population at one stable optimal value • Directional selection transforms the value of a trait by increasing

the frequency of individuals closer to a distant optimum • Disruptive selection increases the frequency of large and small values of a trait at

the expense of intermediate values • Balancing selection selects the optimal compromise among several constraints At their core, all forms of selection involve individuals with inherited differences in fitness competing within the same population. This competition is about fitness as measured by survival rates, fecundity, or some other trait that correlates with fitness. The "winner" of the competition is positively selected, and its genotype increases in frequency; on the other hand, the "loser" is negatively selected, and the frequency of its genotype decreases. Thus, negative selection and positive selection cannot be separated. To make communication easier, however, scientists talk about positive selection when the focus of a particular study is on an increase in rare variants that improve optimal fitness, and they speak of negative selection when the focus is on the removal of harmful variants.

55 Dr. Laurence Loewe (University of Edinburgh, Scotland, UK) © Nature Negative Selection -‐ http://www.nature.com/scitable/topicpage/Negative-‐Selection-‐1136


1.6 Historical Background56 on Darwin’s Theory of Evolution Darwin's ideas were inspired by:

1. The theory of Principles of Geology by Charles Lyell promoted the idea that simple weak forces could act continuously over long periods of time to produce radical changes in the Earth's landscape.

2. The observations that he had made on the Beagle voyage, 3. The work of a political economist, the Reverend Thomas Malthus, who in An

Essay on the Principle of Population, noted that population (if unchecked) increases exponentially, whereas the food supply grows only arithmetically; thus, inevitable limitations of resources would have demographic implications, leading to a "struggle for existence".

The success of uniformitarianism theory raised awareness of the vast scale of geological time and made plausible the idea that tiny, virtually imperceptible changes in successive generations could produce consequences on the scale of differences between species. Uniformitarianism was formulated by Scottish naturalists in the late 18th century, starting with the work of the geologist James Hutton, which was refined by John Playfair and popularized by Charles Lyell's Principles of Geology in 1830. When Darwin read Malthus in 1838 he was already primed by his work as a naturalist to appreciate the "struggle for existence" in nature and it struck him that as population outgrew resources, "favorable variations would tend to be preserved, and unfavorable ones to be destroyed. The result of this would be the formation of new species.

1.6.1 Pre Darwinian Theories Several ancient philosophers expressed the idea that nature produces a huge variety of creatures, randomly, and that only those creatures that manage to provide for themselves and reproduce successfully survive; well-‐known examples include Empedocles and his intellectual successor, the Roman poet Lucretius

Empedocles' idea that organisms arose entirely by the incidental workings of causes such as heat and cold was criticized by Aristotle in Book II of Physics. He posited natural teleology in its place. He believed that form was achieved for a purpose, citing the regularity of heredity in species as proof. The struggle for existence was later described by Islamic writer Al-‐Jahiz in the 9th century, who argued that environmental factors influence animals to develop new characteristics to ensure survival. According to Rainow, the 11th century scholar Abu Rayhan Biruni described the idea of artificial selection and argued that nature works in much the same way.

56 Background on Darwin’s work


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Pierre Louis Maupertuis reintroduced the classical arguments in the 18th century along with others; including Charles Darwin's grandfather Erasmus Darwin. While these forerunners had an influence on Darwinism, they later had little influence on the trajectory of evolutionary thought after Charles Darwin.

1.6.2 Refuting Creationist claim on Darwin’s history According to Archbishop James Ussher’s57 estimate based on genealogy in the Bible Earth got created around the year 4004 B.C. That put the age of Earth around 6000 years old. Lord Kelvin58 (famous physicist at that time) calculated that the age of Earth is around 40 (max) million years. Kelvin’s estimate came from physics of cooling of the Earth and the Sun. Darwin felt this age has to be wrong, because with 40 million years he realized that evolution is not possible for so many diverse amounts of species you observe on planet Earth. Lord Kelvin was against the concept of Darwin’s Evolution and he felt his calculation of Earth’s age refutes Darwin’s theory of Evolution and point towards the spontaneous creation of species by God. Now let us look at Hussain’s perspective on Darwinian History.

The key issue over here is, his lack of understanding of Darwin’s “On Origin of Species”. It’s a collection of theories, which results in describing the Evolution of Species. Hussain’s lack of knowledge in understanding Natural Selection and its process and the environment required (longer period of time and Earth’s geological time) for Evolution, compounded his blindness to the theory and results in erroneous depiction of history. Last line is the most interesting one. Hussain says, Evolutionists like Stephen Gould supports Creationism. In the next section we will evaluate this and understand the perspectives of these scientists. Here, it looks like Hussain supports Creationism and not Intelligent Design and don’t even think about Evolution!

57 Archbishop James Ussher – Wikipedia 58 Lord Kelvin – Wikipedia


1.7 FARM Formula to test Evolution Theory Following diagram shows the history of Earth in 24 hours format. However, most of the creationists don’t believe in this history. They believe the Earth and life is only around 6000 years old!

Most of the creationists argue that Darwin’s theory is not a theory because there are so many missing links in finding the fossils. Checkout page number 5 – Geological Time Line Here is a simple experiment they (creationists) can do to disprove (concept from Richard Dawkins God Delusion) the theory of Evolution. As per the evolution time scale, the order of evolution is as follows in simple terms (24 hour time scale).

Type Bacteria59 Jelly Fish60 Fish61 Amphibians62 Reptiles63 Mammals64 24 hour Time Scale 8:48 pm 9:00 pm 10:00 pm 10:45 pm 11:40 pm Fossil Record 3.4 bya 530+ mya 530 mya 39765 mya 340 mya 195 mya

Formula to Test Evolution = Fish > Amphibian > Reptiles > Mammals They (creationist) need to find just ONE fossil out of order. Means if they find a fossil of any Mammal older than Amphibian fossil or Fish Fossil then evolution collapses like a pack of cards. 59 Discovery Channel: Oldest fossil of bacteria, living 3.4 billion years were found in Australia 60 National Geographic : Oldest Jelly Fish fossil record, half a billion years 61 BBC News: Oldest fish fossil record 530 million years ago 62 Berkeley University: Oldest Amphibian fossil record 368 million years 63 New York Times: Oldest Reptile fossil record 340 million years 64 Harvard University: Oldest Mammal fossil record 195 million years 65 National Geographic – Oldest land walker tracks found Jan 6, 2010


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Just ONE fossil that’s all, any creationists required to break this evolution pattern! So, instead of asking for the missing link, they should find just one fossil, just one fossil out of the order, which will end the debate forever. Instead what they do is to catch on to some out of context statement. The best example of this is the IDA fossil discovery. Initial interpretations from the scientist placed that fossil in the Homo sapiens evolution branch. However, after the careful analysis and study, they realized that it fits more accurately in the Lemur branch. Creationist will just simply forget the fact that the IDA fossil has moved on to another branch after extensive study and its still part of the Tree of Life. What this means is all the fossils scientists finds is actually increasing the proofs for Evolution and not the other way around.

1.7.1 Refuting Creationist claim on Natural Selection: Analyze geological time The fossil record clearly indicates a progression and divergence of species over a period of long time, clearly indicating the three key elements of Natural Selection (Variation, Selection and Time). If Hussain says that Natural Selection doesn’t work then how will he explain this fossil record and geological time line?

1. Single Cell 2. Multi Cell 3. Fish 4. Amphibians 5. Reptiles 6. Mammals

To prove that this is wrong Hussain or a creationist needs to find just ONE fossil of human before or at the time of fish evolution. Just ONE fossil that’s all they need to find rather than asking for missing links. Can’t they find just ONE fossil in 150 years? There is no concept of missing link in evolutionary biology. Every fossil found is been added to the existing branch or may be creating a new branch resulting in more proof for evolution. So, why don’t all these creationists spend their time searching for that ONE fossil which is the Holy Grail of creationism?


1.8 Comparing Two Religious Views against Science (Evolution)

Creationism66 Intelligent Design67 Science – Darwin’s Evolution68 God created all species as is. Bible Genesis

-‐ Irreducible Complexity Ex: Bacterial flagellum, By Michael Behe -‐ Specified Complexity By William Dembski

-‐ Fine Tuned Universe -‐ Intelligent Designer

-‐ Natural Selection69 based on external pressures modifies a species over a period of time. Chapter IV, Page 77

Belief in the literal interpretation of the account of the creation of the universe and of all living things related in the Bible.

-‐ Some ID Scientists accepts Evolution partially

-‐ Accepts Darwin’s Natural Selection

-‐ Accepts Darwin’s Common Descent

-‐ This process would connect all life forms via their descent from common ancestors70. Chapter XIV, Page 477

Creation means that various forms of life began abruptly through the agency of an Intelligent creator with their distinctive features already intact -‐-‐ fish with fins and scales, birds with feathers, beaks and wings etc. (The Design of Life, William Dembski, p28, Dover Exhibit #775)

Intelligent Design means that various forms of life began abruptly through the agency of an intelligent creator with their distinctive features already intact -‐-‐ fish with fins and scales, birds with feathers, beaks and wings etc. Of Pandas and People, 1993, Page 99-‐100

-‐ Therefore all the organic beings have descended from one primordial form71, into which life was first breathed. Chapter XV, Page 502

MIRACLES REQUIRED* MIRACLES REQUIRED* NO MIRACLES REQUIRED * Miracles required because scientifically it’s an illogical process. If there is no Evolution then what else can be potentially a different scientific view. There is NONE! Wait a minute there is an alternate hypothesis. All living species evolve from Single cell to the complex species, which means it’s not a tree with a common descent instead, all species evolved in parallel! In effect this is more complex than Natural Selection and a common descent. Apply Occam’s razor72 here Darwin’s Theory of Evolution wins! So, what is established here is Evolution can be the ONLY logical way of explaining the Origin of Species without invoking any miracles! 66 Definition of Creationist Theory http://www.thefreedictionary.com/creationism 67 Intelligent Design 68 On Origin of Species, Charles Darwin, Signet Classics 150th Anniversary Edition 69 On Origin of Species, Charles Darwin, Signet Classics 150th Anniversary Edition, Page 77 70 On Origin of Species, Charles Darwin, Signet Classics 150th Anniversary Edition, Page 477 71 On Origin of Species, Charles Darwin, Signet Classics 150th Anniversary Edition, Page 502 72 Occam’s Razor -‐ It is a principle stating that among competing hypotheses, the one, which makes the fewest assumptions, should be selected. http://en.wikipedia.org/wiki/Occam's_razor


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That’s why Scientists across the World considers Darwin’s work as an extra ordinary break through at par with Einstein’s Theory of Relativity and Quantum Mechanics. Any other view other than Evolution requires miracles. Now that’s faith. So, the critical point is no point in comparing Science with Religion (Faith).

1.8.1 Creationism73 It is the religious belief that humanity, life, the Earth, and the universe are the creation of a supernatural being, most often referring to the Abrahamic God. As science developed from the 18th century onwards, various views developed which aimed to reconcile science with the Abrahamic creation narrative. At this time those holding that species had been created separately (such as Philip Gosse in 1847) were generally called "advocates of creation" but they were occasionally called "creationists".

1.8.2 Intelligent design74 (ID) It is a form of creationism promulgated by the Discovery Institute. The Institute defines it as the proposition that "certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection." It is a contemporary adaptation of the traditional teleological argument for the existence of God, presented by its advocates as "an evidence-‐based scientific theory about life's origins" rather than "a religious-‐based idea. Irreducible Complexity, proposed by Michael Behe, is the key component of Intelligent Design. In the next section we will try to understand the concept of Irreducible Complexity.

1.8.3 Irreducible Complexity75 (IC) – By Michael Behe Michael J Behe76 introduced the concept of Irreducible Complexity in his book Darwin’s Black Box.77 Let us understand that from Behe’s on words from Black Box. “By irreducibly complex I mean a single system composed of several well-‐matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning. An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional. An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution”. -‐ Michael Behe, Darwin’s Black Box, Page no, 39

73 Creationism 74 Intelligent Design 75 Irreducible Complexity 76 Michael J Behe, Biochemistry, Discovery Institute, USA 77 Darwin’s Black Box by Michael J Behe


The Current Intelligent Design movement rides on Behe’s Irreducible Complexity idea. I know this is not part of this discussion as per Hussain’s article, however, I would like to briefly mention this case to have a complete picture on alternate theories to Evolution. Unfortunately both Creationism and Intelligent Design revolves around a Supreme Agent who supports the origin of species, which is clearly not science, but faith. Like I said before Faith and Science is not a subject I would like to debate here. However, existence of God can be a separate debate. Now let us understand exactly what Irreducible complexity means:

1. The cell contains Biochemical machines in which the loss of a single component may abolish function (i.e., are Irreducibly Complex)

2. And any Irreducibly Complex structure that is missing a part is by definition non-‐functional, leaving natural selection with nothing to select for.

3. Therefore, irreducibly complex structures cannot be produced by natural selection.

4. Therefore, they must be the products of Intelligent Design (= evidence for design)

1.8.4 Bacterial Flagellum – Fallen case of Irreducible Complexity The Bacterial Flagellum is the classic case show cased by Michael Behe, explaining that, this system is created with around 50 proteins and if 1 protein is missing then rest of the proteins where useless for the species, so there is nothing for the natural selection to select, for the flagellum to evolve. Following images shows the components of bacterial flagellum and how the sub components used for other things Bacterial Flagellum78 Other Usage of Flagellum components

The above diagram clearly shows how Michael Behe’s argument falls flat on Irreducible complexity with Flagellum. As per Behe there should not be any use with the subcomponents of Bacterial flagellum.

78 Image courtesy Kenneth Miller lecture in Sept 27, 2006, HHMI headquarters for High School students from Loudon County, VA, USA


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This was the critical issue Behe show cased in the famous Kitzmiller Vs. Dover Area School District79 case80 2005, Philadelphia, USA. Kenneth Miller81 testified in the court talking about Type III Secretion System82 (TTSS), made up of around 10 proteins, which is also part of Bacterial Flagellum. Now the question whether TTSS is a precursor to Flagellum or not is something needs to be verified. However, the point in Irreducible Complexity is if one of the protein is not available then rest of the proteins are completely non functional, and that’s the point which breaks concept of Irreducible Complexity with TTSS. Watch the 2 hours of “Great Debate” 83 between Kenneth Miller and Michael Behe on the same subject. (YouTube videos divided into 3 parts). That’s the first pillar (Irreducible Complexity) of Intelligent Design, now its time for us to focus on the second pillar of Intelligent Design, i.e., Specified Complexity by William Dembski. We will look at Dembski’s Explanatory Filter, which is created to discovering Intelligent Design in nature. We will go through the filter using few examples and see how the filter stands upto the test.

79 Kitzmiller vs. Dover Area School District 80 Judge rules against Intelligent Design, Dec 20th, 2005, Supreme Court, Philadelphia, USA 81 Kenneth R Miller, Brown University, USA 82 Type III Secretion System 83 From Great Debate Kenneth Miller Vs. Michael Behe (Part 3)


1.8.5 Specified Complexity84 (SC) – By William Dembski85 Specified Complexity is another key idea in Intelligent Design proposed by William Dembski. The concept is intended to formalize a property that singles out patterns that are both specified and complex. Dembski states that specified complexity is a reliable marker of design by an intelligent agent, a central tenet to intelligent design and which Dembski argues for in opposition to modern evolutionary theory. Some regard specified complexity as mathematically unsound claiming that it has not been the basis for further independent work in information theory, complexity theory, or biology. Specified complexity is one of the two main arguments used by intelligent design proponents, the other being irreducible complexity. Following is Dembski‘s explanatory filter86 to detect Intelligent Design in the nature.

One of the key (faulty) assumptions Dembski makes is that if something cant be explained at that particular moment by science then it goes into the realm of Specified Complexity. It’s assuming that science has mastered everything of that particular event and there is nothing more to learn. Its best to explain this filter with a case and see if we can infer the design, if the event has specification, which will remove Natural Cause and Chance.

84 Specified Complexity by William Dembski – Wikipedia 85 William Dembski – Wikipedia 86 The Design Inference by William Dembski, Page 37 – Wikipedia


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1.8.6 Example using Dembski Explanatory Filter to detect Design Fairy Ring87 It is a naturally occurring ring or arc of mushrooms. The rings may grow to over 10 meters (33 ft) in diameter, and they become stable over time as the fungus grows and seeks food underground. They are found mainly in forested areas, but also appear in grasslands or rangelands. Fairy rings are detectable by sporocarps in rings or arcs, as well as by a necrotic zone (dead grass), or a ring of dark green grass. If these manifestations are visible a fairy fungus mycelium is likely to be present in the ring or arc underneath. Fairy rings also occupy a prominent place in European folklore as the location of gateways into elfin kingdoms, or places where elves gather and dance. According to the folklore, a fairy ring appears when a fairy, pixie, or elf appears. It will disappear without trace in less than five days, but if an observer waits for the elf to return to the ring, he or she may be able to capture it. Now let us apply Dembski Explanatory Filter over here and do time travel to Europe in early 1800s, and assume that you are peasant working on a field and happened to see the Fairy Ring.

87 Fairy Ring – Wikipedia


Now let us look at what modern science has to say (from Britannica Encyclopedia88). Fairy Ring a naturally occurring circular ring of mushrooms on a lawn or other location. A fairy ring starts when the mycelium (spawn) of a mushroom falls in a favorable spot and sends out a subterranean network of fine, tubular threads called hyphae. The hyphae grow out from the spore evenly in all directions, forming a circular mat of underground hyphal threads. The mushrooms that grow up from this circular underground mat form a similar pattern above ground. Gradually the underground mycelium at the center of the circle dies out. Its living outer edges, however, keep growing year by year, and hence the diameter of the ring gradually increases. Over time the ring’s underground segments die out, until the ring form on the surface can no longer be discerned. Krebs Cycle89 Following extract from Kenneth Miller web site (Web link available in footnote).. The Krebs cycle, an intricate biochemical pathway consisting of nine enzymes and a number of cofactors that occupies center stage in the pathways of cellular metabolism. The Krebs cycle is "real," "complex," and "biochemical." Does it also present a problem for evolution? Apparently yes, according to the authors of a 1996 paper in the Journal of Molecular evolution, who wrote:

"The Krebs cycle has been frequently quoted as a key problem in the evolution of living cells, hard to explain by Darwin’s natural selection: How could natural selection explain the building of a complicated structure in toto, when the intermediate stages have no obvious fitness functionality? (Melendez-‐Hevia, Wadell, and Cascante 1996)

Where intelligent design theorists throw up their hands and declare defeat for evolution, however, these researchers decided to do the hard scientific work of analyzing the components of the cycle, and seeing if any of them might have been selected for other biochemical tasks. What they found should be a lesson to anyone who asserts that evolution can only act by direct selection for a final function. In fact, nearly all of the proteins of the complex cycle can serve different biochemical purposes within the cell, making it possible to explain in detail how they evolved:

In the Krebs cycle problem the intermediary stages were also useful, but for different purposes, and, therefore, its complete design was a very clear case of opportunism. . . . the Krebs cycle was built through the process that Jacob (1977) called ‘‘evolution by molecular tinkering,’’ stating that evolution does not produce novelties from scratch: It works on what already exists. The most novel result of our analysis is seeing how, with minimal new material, evolution created the most important pathway of metabolism, achieving the best chemically possible design. In this case, a chemical engineer who was looking for the best design of the process could not have found a better design than the cycle which works in living cells." (Melendez-‐Hevia, Wadell, and Cascante 1996)

Since this paper appeared, a study based on genomic DNA sequences has confirmed the validity of this approach (Huynen, Dandekar, and Bork 1999). By contrast, how would intelligent design/creationists have approached the Krebs cycle?

88 Fairy Ring – Britannic Encyclopedia 89 Krebs Cycle, Kenneth Miller


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Using Dembski's calculations as our guide, we would first determine the amino acid sequences of each of the proteins of the cycle, and then calculate the probability of their spontaneous assembly. When this is done, an origination probability of less than 10 -‐400 is the result. Therefore, the result of applying "design" as a predictive science would have told both groups of researchers that their ultimately successful studies would have been fruitless, since the probability of spontaneous assembly falls below the "universal probability bound." When you try to understand all these ID philosophies it’s time we need to remember the English Theologian William Paley90 creator of the famous watchmaker91 analogy. In 1802, Paley wrote (in Natural Theology), if we find a pocket watch in a field, we immediately infer that it was produced not by natural process acting blindly but by a designing human intellect. So, the argument of Intelligent Design has roots even before the Darwin published Origin of Species. It’s an interesting journey from Blind Watchmaker to Irreducible Complexity & Specified Complexity. If you look at these philosophies, what is evident is something against the scientific mind. If something is unknown or unable to grasp for a person then he/she attributes that to a Designer, and then the rest of the world must follow his conclusion blindly. That’s not science, that’s blind faith and they can’t think beyond the obvious. Science is all about having a curious mind and asking why, when others give up their hands saying it’s impossible or attribute to God’s miracle. After summarizing some key fossil evidence in Earth’s geological time frame, we will focus on Hussain’s interpretation of famous scientists quotes and his intentions on quoting them. In the last section we will look at some prominent evidences in support of Evolution both in Micro and Macro world of evolution.

90 William Paley – Wikipedia 91 Watchmaker Analogy -‐ Wikipedia


1.9 Verdict of prominent cases of Creationism Vs. Evolution in US Courts92

1.9.1 Supreme Court of the United States, Epperson v. Arkansas, 1968

"Government in our democracy, state and national, must be neutral in matters of religious theory, doctrine, and practice. It may not be hostile to any religion or to the advocacy of non-‐religion, and it may not aid, foster, or promote one religion or religious theory against another or even against the militant opposite."

1.9.2 Supreme Court of the United States, Edwards v. Aguillard, 1987

"[The] primary purpose [of the Louisiana 'Creation Act,' which required the teaching of 'creation science' together with evolution in public schools] was to change the public school science curriculum to provide persuasive advantage to a particular religious doctrine that rejects the factual basis of evolution in its entirety. Thus, the Act is designed either to promote the theory of creation science that embodies a particular religious tenet or to prohibit the teaching of a scientific theory disfavored by certain religious sects. In either case, the Act violates the First Amendment."

1.9.3 Kitzmiller v. Dover Area School District, 2005

"[W]e find that ID [intelligent design] is not science and cannot be adjudged a valid, accepted scientific theory, as it has failed to publish in peer-‐reviewed journals, engage in research and testing, and gain acceptance in the scientific community. ID, as noted, is grounded in theology, not science…. Moreover, ID’s backers have sought to avoid the scientific scrutiny which we have now determined that it cannot withstand by advocating that the controversy, but not ID itself, should be taught in science class. This tactic is at best disingenuous, and at worst a canard. The goal of the IDM [intelligent design movement] is not to encourage critical thought, but to foment a revolution which would supplant evolutionary theory with ID."

92 http://www.nationalacademies.org/evolution/Excerpts.html


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2. Wrong interpretation of Science and Scientist’s Quotes The most critical weapon creationist uses is misquoting prominent scientists without understanding science and their statements. Here is an interesting example from Hussain’s article on Evolution

2.1 Stephen Jay Gould93, Niles Eldredge94

Along with many other researchers in the field, Gould's works were sometimes deliberately taken out of context by creationists95 as "proof" that scientists no longer understood how organisms evolved. Gould himself corrected some of these misinterpretations and distortions of his writings in later works.

2.1.1 Refuting Creationist claim that Evolution is dead as per Stephen Jay Gould The following essay originally appeared in The New Yorker, Dec. 13, 1999 FOUR months ago, when the Kansas Board of Education voted to cut evolution from the mandatory science curriculum, few people were more outraged than Stephen Jay

93 Steven Jay Gould, Paleontologist, Evolutionary Biologist, USA 94 Niles Eldredge, Paleontologist, USA 95 Creationism -‐ http://en.wikipedia.org/wiki/Creationism


Gould. Teaching biology without evolution is "like teaching English but making grammar optional," Gould said. The Kansas decision reeked of "absurdity" and "ignorance" and was a national embarrassment. The question of whether to teach evolution "only comes up in this crazy country," he told an audience at the University of Kansas after the decision. Check the statements from Stephen Jay Gould “Evolution as Fact and Theory” (May 1981)96.

We proposed the theory of punctuated equilibrium largely to provide a different explanation for pervasive trends in the fossil record. Trends, we argued, cannot be attributed to gradual transformation within lineages, but must arise from the different success of certain kinds of species. A trend, we argued, is more like climbing a flight of stairs (punctuated and stasis) than rolling up an inclined plane.

Since we proposed punctuated equilibria to explain trends, it is infuriating to be quoted again and again by creationists—whether through design or stupidity, I do not know—as admitting that the fossil record includes no transitional forms. Transitional forms are generally lacking at the species level, but they are abundant between larger groups. ……….

I am both angry at and amused by the creationists; but mostly I am deeply sad97…. Evolution is one of the half dozen “great ideas” developed by science. Now over here, Hussain never tried to learn what the “theory of punctuated equilibrium” is all about, and the funny part is, he gave a new definition on that theory! Hearing bits and pieces information resulted in him concluding that as per Stephen Jay Gould – Darwin’s Evolution theory is dead!

How ridiculous is his statement! Science is not bits and pieces of information; it requires a focused study without a prejudiced mind. Currently I am reading N M Hussain’s article as an interesting science fiction . But I don’t see any Science in it unfortunately.

96 Stephen Jay Gould, "Evolution as Fact and Theory," Discover 2 (May 1981): 34-‐37; From Hen's Teeth and Horse's Toes, New York: W. W. Norton & Company, 1994, Page 260. 97 Stephen Jay Gould, From Hen's Teeth and Horse's Toes, New York: W. W. Norton & Company, 1994, Page 261, Para 2, line no: 1 and Para 3 line no.4


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Lets move forward analyze some more content from Hussain’s article talking Stephen Gould and some other prominent paleontologist and molecular biologist. Hussain has very specific comments on their contribution to science and their perspectives on Darwin’s Theory of Evolution. We will evaluate the new theories as well as these scientist’s perspectives on the Theory of Evolution.

Here is the summary of the Book Hen’s Teeth and Horse’s98 Toes, By Stephen Jay Gould Over a century after Darwin published the Origin of Species, Darwinian theory is in a 'vibrantly healthy state, ' writes Stephen Jay Gould, its most engaging and illuminating exponent. Exploring the 'peculiar and mysterious particulars of nature, ' Gould introduces the reader to some of the many and wonderful manifestations of evolutionary biology.

2.2. Steven M Stanley99 Another Scientist Hussain quote is Steven M Stanley the world famous paleontologist. Let us look what he (Hussain) has to say about him.

98 Flipkart.com -‐ Hen's Tooth and Horse's Toes By Stephen Jay Gould 99 Steven M Stanley, Paleontologist, Evolutionary Biologist, University of Hawaii, USA


Here Hussain makes an astonishing error. He says, as per the observations of humans, the species remain static without any evolution. He thinks that macroevolution must happen in a human time scale! However, latest molecular study in the case of eradicating malaria shows that in the micro world, humans and malaria are evolving right in front of our eyes. Check out the evidence section. Stanley along with Niles Eldredge and S. J. Gould, has been one of the principal advocates of punctuational rate in evolution. He elaborated punctuated equilibrium prior to Gould, in 1975, and presented further research on the matter in 1981 and 1982. Do I have to say anything more? They were not against Evolution, they come out with a new theory to explain the fossil record (as per Gould), rather than saying evolution is not correct. It seems Hussain is desperately trying to hold on to some scientist to prove that Evolution (Science) is wrong and God created all these species. Stanley’s interpretation of the vertebrate fossil record as displaying a punctuational nature has been severely questioned by the work of Philip Gingerich (1980, 1982, 1983) and Robert Carroll (1988). Stanley's arguments that the process of punctuated equilibrium is inconsistent with the Neodarwinian paradigm of gradualistic evolution, has been most effectively challenged by Mayr (1982). The above model is the way Science works. Scientist try to get the best theory to explain the Natural phenomena rather than attributing to God.


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If Hussain translate the above two paragraphs he has written (into English) and show it to Gould and Stanley they will get a shock of their life. This is exactly the sentiment Gould shown against creationist. Creationists are bunch of people who don’t have analytical capabilities. Otherwise they would try to spend time to understand what’s Punctuated Equilibrium proposed by Gould and team. What Stanley, Stephen Jay Gould and Niles Eldredge talked about is not that Natural Selection doesn’t work. They emphasized a method to explain the fossil records with their theory, which as per Gould itself is a model of gradualism when you look at the evolution at Geological time frame. Darwin himself acknowledges in his book “On the Origin of species” that there will be variation in rate of change from species to species, checkout the section Multiple meanings of Gradualism.

2.3 Theories to explain the progress of Evolution Anyway, here is a quick summary on Punctuated Equilibrium, Multiple meanings of gradualism, and Quantum Evolution.

2.3.1 Punctuated equilibrium It is a theory popularized by Stephen Jay Gould and Niles Eldredge. The theory postulates that evolutionary change is not constant but that speciation may occur rapidly and the species then change little for long periods of time. The theory explains the patterns shown in the fossil record.

2.3.2 Multiple meanings of gradualism

Punctuated equilibrium is often portrayed to oppose the concept of gradualism, when it is actually a form of gradualism100. This is because even though evolutionary change appears instantaneous between geological sediments, change is still occurring incrementally, with no great change from one generation to the next. To this end, Gould later commented, "Most of our paleontological colleagues missed this insight because they had not studied evolutionary theory and either did not know about allopatric speciation or had not considered its translation to geological time.

Now let us look at what Darwin has to say on varying rate of change as per Gould, Eldredge (and even Stanley). Charles Darwin was influenced by Lyell's Principles of Geology, which explained both uniformitarian methodology and theory. The concept of gradualism was promoted by his friend Charles Lyell. It is often incorrectly assumed that he (Darwin) insisted that the rate of change must be constant, or nearly so.

100 Richard Dawkins, The Blind Watch Maker (1996) page 224-‐252


Species of different genera and classes have not changed at the same rate, or in the same degree.


In the fifth edition Darwin wrote “Many species when once formed never undergo any further change but become extinct without leaving modified descendants; and the periods during which species have undergone modifications, though long as measure by years have probably been short in comparison with the periods during which they have retained the same form.” -‐ Charles Darwin, Chapter XV “Recapitulation and Conclusion”, On the Origin of Species, Page 483 So, to summarize what happened in the last two pages (regarding Gould, Stanley) is that, they have come up with a theory to explain observed fossil record with the theory punctuated equilibrium – which says the rate of change due to Natural selection will not be linear. I am really shocked the way Hussain twisted a new explanation completely out of context. If you remember, this review got started with the quote from Charles Lyell101 point no. 6. This is a classic example of reading bits and pieces of info from creationist sites and trying to create an article out of it.

2.3.3 Quantum evolution Quantum evolution was a controversial hypothesis advanced by Columbia University paleontologist George Gaylord Simpson, who was regarded by Stephen Jay Gould as "the greatest and most biologically astute paleontologist of the twentieth century." Simpson's conjecture was that according to the geological record, on very rare occasions evolution would proceed very rapidly to form entirely new families, orders, and classes of organisms. This hypothesis differs from punctuated equilibrium in many respects. First, punctuated equilibrium was much more modest in scope, in that it was addressing evolution specifically at the species level. Simpson's idea was principally concerned with evolution at higher taxonomic groups. Second, Eldredge and Gould relied upon an entirely different mechanism. Where Simpson relied upon a synergistic interaction between genetic drift and a shift in the adaptive fitness landscape. According to Simpson, evolutionary rates differ from group to group and even among closely related lineages. These different rates of evolutionary change were designated by Simpson as horotelic (medium tempo), bradytelic (slow tempo), and tachytelic (rapid tempo). Quantum evolution differed from these styles of

101 Charles Lyell, British Geologist and Lawyer, (1797-‐1875)


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change in that it involved a drastic shift in the adaptive zones of certain classes of animals. The word "quantum" therefore refers to an "all-‐or-‐none reaction," where transitional forms are particularly unstable, and perished rapidly and completely. According to Simpson (1944) quantum evolution relied heavily upon Sewall Wright's theory of random genetic drift. Simpson believed that major evolutionary transitions would arise when small populations—isolated and limited from gene flow—would fixate upon unusual gene combinations I have a section dedicated to understand what’s genetic drift and how it compares with Natural Selection. Over here these scientists are trying to figure out the real model of evolution in genes and how they can be compared to macroevolution. If some one is focused on quoting scientists instead of trying to figure their theories what results in is nothing but a state of words diarrhea. People with prejudiced mind will never understand anything new.

2.3.4 Creationist interpretation on Gould’s Punctuated Equilibrium Theory Following section (underlined in red) explains Hussain’s interpretation of Punctuated Equilibrium theory.

Under the camouflage of Punctuated Equilibria theory by Gould, Hussain says that all these scientists declared that evolution cant happen because of Natural Selection. If


Hussain lived in a developed country, he will be sued for misrepresenting the facts and twisting the facts. Here Hussain’s proclaims in a sarcastic tone that all the work in Evolutionary Biology is a waste (the last line). If you need to master all the different subjects in Evolutionary Biology, you will end up having atleast a dozen different Ph. D.s to master everything. Without understanding genetic science, without understand natural selection, right in the first chapter of the article he vociferously claims that all the books on Evolution is nothing but a waste.

Now let us look what’s Stephen Jay Gould has to say (the Author of the Theory) : Check the statements from Stephen Jay Gould “Evolution as Fact and Theory” (May 1981)102.

Following extract from "Evolution as Fact and Theory," by Stephen Jay Gould, May 1981; from Hen's Teeth and Horse's Toes, New York: W. W. Norton & Company, 1994, pp. 253-‐262.

We proposed the theory of punctuated equilibrium 103 largely to provide a different explanation for pervasive trends in the fossil record. Trends, we argued, cannot be attributed to gradual transformation within lineages, but must arise from the different success of certain kinds of species. A trend, we argued, is more like climbing a flight of stairs (punctuated and stasis) than rolling up an inclined plane.

Since we proposed punctuated equilibria to explain trends, it is infuriating to be quoted again and again by creationists—whether through design or stupidity, I do not know—as admitting that the fossil record includes no transitional forms. Transitional forms are generally lacking at the species level, but they are abundant between larger groups. ……….

I am both angry at and amused by the creationists; but mostly I am deeply sad. Now let us see what Charles Darwin has to say on gradualism. Species of different genera and classes have not changed at the same rate, or in the same degree. 102 Stephen Jay Gould, "Evolution as Fact and Theory," Discover 2 (May 1981): 34-‐37; From Hen's Teeth and Horse's Toes, New York: W. W. Norton & Company, 1994, pp. 253-‐262 103 Stephen Jay Gould, "Evolution as Fact and Theory," May 1981; from Hen's Teeth and Horse's Toes, New York: W. W. Norton & Company, 1994, pp. 253-‐262. ]


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In the fifth edition Darwin wrote “Many species when once formed never undergo any further change but become extinct without leaving modified descendants; and the periods during which species have undergone modifications, though long as measure by years have probably been short in comparison with the periods during which they have retained the same form.” -‐ Charles Darwin, Chapter XV “Recapitulation and Conclusion”, On the Origin of Species, Page 483 Without understanding the theory of Punctuated Equilibrium, Hussain concludes that Gould’s theory is getting closer to the concept of “God created all the species”! On the question of teaching Creationism in schools -‐ Washington Post104 It's all enough to set another Harvard man, the author and Harvard biology professor Stephen Jay Gould, to vibrating. "It's intellectually so disappointing and so absurd," Gould says. "It's like teaching English but making grammar optional."

There is a central "truth," embraced by virtually every mainstream scientist worldwide: that the cosmos and the Earth were created billions of years ago, and that life evolved from one-‐celled animals to modern humans.

That these overarching concepts are pockmarked with unexplained gaps and phenomena, and subject to constant revision and debate, is but the nature of the scientific method.

N M Hussain has reached the desperate state to declare Gould as a creationist! Here is Stephen Jay Gould’s105 advice on debating with creationist Winning is not what the creationists realistically aspire to. For them, it is sufficient that the debate happens at all. They need the publicity. We don't. To the gullible public, which is their natural constituency, it is enough that their man is seen sharing a platform with a real scientist. "There must be something in creationism, or Dr So-‐and-‐So would not have agreed to debate it on equal terms." Inevitably, when you turn down the invitation you will be accused of cowardice, or of inability to

104 Washington Post Sept 6, 1999 Creationism the debate fails to evolve 105 Guardian Newspaper Aug 19th, 2008 – Richard Dawkins quoting Gould while debunking Harun Yahya’s Atlas of Creation


defend your own beliefs. But that is better than supplying the creationists with what they crave: the oxygen of respectability in the world of real science. The above quotes from Stephen Jay Gould clearly show the intentions of creationists. They are nothing but annoying mosquitos, which can disturb a night’s sleep. They come with the mask of knowing science, however, when you start asking them questions, they will hide behind their respective religions.

2.4 Motoo Kimura106 The next key scientist Hussain focuses on is the Motoo Kimura, A Japanese biologist best known for introducing the Neutral Theory of Molecular Evolution.

Checkout the last paragraph Now before we get into Motoo Kimura’s Neutral Theory of Molecular Evolution when need to study some fundamentals, Like Population Genetics, McDonald-‐Kreitman test and finally move on to Neutral Theory of Molecular Evolution.

2.5 Theories on Molecular Evolution

2.5.1 Population genetics107 It is the study of gene frequency distribution and change under the influence of the four main evolutionary processes: natural selection, genetic drift, mutation and gene flow.

106 Motoo Kimura, Japanese Biologist, Known for Neutral Theory of Molecular Evolution 107 Statistical Genetics


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2.5.2 Genetic Drift108 Vs. Natural Selection The law of large numbers predicts little change over time due to genetic drift when the population is large. When the reproductive population is small, however, the effects of sampling error can alter the allele (gene) frequencies significantly. Genetic drift is therefore considered to be a consequential mechanism of evolutionary change primarily within small, isolated populations. Although both processes affect evolution, genetic drift operates randomly while natural selection functions non-‐randomly. While natural selection has a direction, guiding evolution towards heritable adaptations to the current environment, genetic drift has no direction and is guided only by the mathematics of chance. In natural populations, genetic drift and natural selection do not act in isolation; both forces are always at play. However, the degree to which alleles are affected by drift or selection varies according to population size. The magnitude of drift on allele frequencies per generation is larger in small populations.

2.5.3 McDonald–Kreitman test109 In statistical genetics, the McDonald–Kreitman test looks for ancient selection over long periods, as opposed to the steady accumulation of mutations that confer no selective advantage predicted by the neutral theory. It was first devised by John H. McDonald and Martin Kreitman in 1991, based on an investigation of differences in amino acid sequence of the alcohol dehydrogenase gene in Drosophila. Nucleotide differences between the coding regions of homologous genes of related species are enumerated and sorted into four categories, as shown below:

Fixed Polymorphic

Synonymous Ds Ps Nonsynonymous Dn Pn Sites are classed as polymorphic if they show any variation within species, while they are classed as fixed if they differ between species but not within them. If the ratio of fixed differences to polymorphisms is much higher for nonsynonymous changes (i.e. Dn/Pn ≫ Ds/Ps), this indicates that genetic changes have been subject to positive selection. The McDonald–Kreitman test itself consists of the G-‐test performed on the numbers in the table above, which would indicate whether the two ratios are significantly different. As an extension of this, Smith and Eyre-‐Walker proposed estimating the

108 Genetic Drift 109 McDonald-‐Kreitman Test


proportion of base substitutions fixed by natural selection, α110 , using a simple formula:

α = 1 – (Ds Pn / Dn Ps) Using this formula, the authors estimated that 45% of amino acid differences between Drosophila simulans and D. yakuba are estimated to have been fixed by selection, while 35% of amino acid differences between primates are estimated to be fixed by selection. Now its time we look into what’s Neutral Theory of Molecular Evolution and see if Hussain’s assumption is correct.

2.5.4 Neutral Theory of molecular evolution111 This theory states that the vast majority of evolutionary changes at the molecular level are caused by random drift of selectively neutral mutants (not affecting fitness). Motoo Kimura introduced the theory in the late 1960s and early 1970s. Neutral theory is compatible with Darwin's theory of evolution by natural selection: adaptive changes are acknowledged as present and important, but hypothesized to be a small minority of all the changes seen fixed in DNA sequences. It’s important to understand the Population genetics (Genetic Drift and Natural Selection) to get clear view of how molecular evolution works. A heated debate arose when Kimura's theory was published, largely revolving around the relative percentages of alleles that are "neutral" versus "non-‐neutral" in any given genome. Contrary to the perception of many onlookers, the debate was not about whether natural selection does occur. Kimura argued that molecular evolution is dominated by selectively neutral evolution but at the phenotypic level, changes in characters were probably dominated by natural selection rather than sampling drift. As of the early 2000s, the neutral theory is widely used as a "null model" for so-‐called null hypothesis testing. However, serious doubt has been cast on the neutral theory by the application of the McDonald-‐Kreitman test to show that a substantial proportion of amino acid changes may be due to selection. Now let us relook at Hussain’s conclusion on Kimura’s work, he concludes that Natural Selection has nothing to do with Origin of Species as per Kimura.

110 Nick G. C. Smith & Adam Eyre-‐Walker (2002). "Adaptive protein evolution in Drosophila" Nature 111 Neutral Theory of molecular evolution


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He conveniently forgets that, he is talking about a statement from Scientists, which is 50 years old! And there wasn’t any progress in Genetic science for the last 50 years. How blind someone can go? Latest genetic science supports with 1000s of evidence for Natural Selection.

2.6 Theodosius Dobzhansky112 It is a 1937 book by the Ukrainian-‐American evolutionary biologist Theodosius Dobzhansky. It is regarded as one of the most important works of the modern evolutionary synthesis. The book popularized the work of population genetics to other biologists, and influenced their appreciation for the genetic basis of evolution.

2.7 Genetics and Origin of Species113 Through his work on the Drosophila pseudoobscura he was able to identify that some populations of this species did not have identical sets of genes. Dobzhansky used experimental breeding in laboratories and gardens, and also surveys related to species in nature to help support the aspects of organic evolution. The data in his book shows the different genetic mutations and chromosomal changes that were observed. All of the results from his experiments support the theory of modern evolutionary synthesis. Now let us look at how Hussain concludes Dobzhansky’s work.

112 Theodosius Dobzhansky, Molecular Biologist 113 Genetics and the Origin of Species: From Darwin to Molecular Biology 60 Years After Dobzhansky Genetics and Origin of Species


Overall Genetics and the Origin of Species shows the importance how genes, mutations, and chromosomal changes influence evolution Dobzhansky’s work was instrumental in spreading the idea that it is through mutations in genes that natural selection takes place. Dobzhansky, A constant defender of Darwinian evolution, he was also, according to his student Francisco J. Ayala, "a religious man" who nonetheless rejected belief in "the existence of a personal God and of life beyond physical death. What this shows that a science, which got developed almost after 80 years, confirmed Darwin’s theory of Natural Selection and that too at micro level, something un-‐thinkable in Darwin’s time. By this time you will have fair idea on how N M Hussain changed and twisted scientists words to prove his theory of creationism. He pretends that he is well versed in all scientific theories related to Evolution. However, some how he is not able to convey that in his article. May be the language (Malayalam, a Language from South India) he is using doesn’t have enough vocabulary to explain his understanding of all theories. Next section focuses on some of the evidences for evolution, Genetic and Macroevolution, which will be required for the conclusion segment. Conclusion segment analyze Hussain’s article, the evidences in this document, and on alternate theories. Apart from these, it has references to key science books from Cosmology, Quantum Physics, Evolution, Genetic Science, and Neuro Science. Its not that reading these books make you an atheist or a firm believer of creationism, however, the objective is to open up your eyes to enjoy the beauty of the nature, grandeur of the universe. People like N M Hussain will even say Big Bang is nothing but a myth and with articles like these they will drive humanity into dark ages. If Hussain is honest enough in whatever he wants to do for understand Science and its role, then he needs to refer to the latest scientific discoveries and evidence and stop focusing on who said what 30-‐40 years ago.


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3. Evidence for Darwin’s Theory of Evolution

3.1 Micro Evolution Evidence

3.1.1 Evidence for Evolution in Human Time Frame: Malaria Vs. Homo Sapiens Malaria pathogen is a critical disease humanity facing today; it infects around 250 million per year and kills almost a million every year. Number of deaths per year is climbing alarmingly and the pathogen is evolving into a state where it started to resist the modern medicine, unless we find a new way of curing malaria in the next 1 year, malaria will ran over humans. Medical science is in a desperate state to save humanity from this deadly pathogen. However, (mostly in malaria infected region) humans evolved to tackle malaria pathogen with the help of a (point) mutation, which has its own side affect. Comparing to the possibility that malaria could wipe out humanity if not checked this mutation still helps with all its negative side effects. This mutation happens in Hemoglobin and due to the shape of the cell after mutation its called sickle cell.

The misshapen red blood cell on the left is caused by a missense mutation and an incorrect amino acid in one of the two polypeptides of hemoglobin. © 2008 by Sinauer Associates, Inc. All rights reserved.

Side effect of sickle is only there if the offspring has inherited sickle cell from both the parents. Single-Base Mutation Associated with Sickle-Cell Anemia114 Sequence for Wild-‐Type Hemoglobin ATG GTG CAC CTG ACT CCT GAG GAG AAG TCT GCC GTT ACT Start Val His Leu Thr Pro Glu Glu Lys Ser Ala Val Thr Sequence for Mutant (Sickle-‐Cell) Hemoglobin ATG GTG CAC CTG ACT CCT GTG GAG AAG TCT GCC GTT ACT Start Val His Leu Thr Pro Val Glu Lys Ser Ala Val Thr The above mutation is found only in the places where malaria is wide spread. Now from a creationist perspective – how do you explain this? From scientific perspective it’s a classic case of Darwin’s Natural Selection. I can imagine the mindset of a creationist now; they are just not in the state of accepting facts. Now read the latest (2012) articles on Malaria and sickle cell anemia from the magazine Nature. Following extract is from the article published in Nature.

114 Nature – Genetic Mutations


Natural Selection: Uncovering Mechanisms of Evolutionary Adaptation to Infectious Disease115 By: Pardis C. Sabeti M.D., D.Phil. (Harvard University, Cambridge, MA) © 2008 Nature Education Citation: Sabeti, P. (2008) Natural selection: uncovering mechanisms of evolutionary adaptation to infectious disease. Nature Education 1(1) The evolutionary link between sickle-‐cell trait and malaria resistance showed that humans can and do adapt. But are the “bugs” that make us sick evolving as well? In the 1940s, J. B. S. Haldane observed that many red blood cell disorders, such as sickle-‐cell anemia and various thalassemias, were prominent in tropical regions where malaria was endemic (Haldane, 1949; Figure 1). Haldane hypothesized that these disorders had become common in these regions because natural selection had acted to increase the prevalence of traits that protect individuals from malaria. Just a few years later, Haldane's so-‐called "malaria hypothesis" was confirmed by researcher A. C. Allison, who demonstrated that the geographical distribution of the sickle-‐cell mutation in the beta hemoglobin gene (HBB) was limited to Africa and correlated with malaria endemicity. Allison further noted that individuals who carried the sickle-‐cell trait were resistant to malaria (Allison, 1954).

Allison's confirmation of Haldane's hypothesis provided the first elucidated example of human adaptation since natural selection had been proposed a century earlier. Today, this and other demonstrations of natural selection help point researchers toward biological mechanisms of resistance to infectious disease. Moreover, such examples also shed light on the ways in which pathogens rapidly evolve to remain agents of human morbidity and mortality. So, why has malaria exerted such strong selective pressure? Scientists now know the answer. Malaria is arguably one of the human population's oldest diseases and greatest causes of morbidity and mortality. Research indicates that the malaria-‐causing parasite Plasmodium falciparum has occurred in human populations for approximately 100,000 years, with a large population expansion in the last 10,000 years as human populations began to move into settlements (Hartl, 2004). P. falciparum, together with the other malaria species, P. vivax, P. malariae, and P. ovale, infects hundreds of millions of people worldwide each year, and kills more than 1 million children annually (World Health

115 Nature :


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Organization, 2000). Because this disease is so devastating, humans have had to evolve adaptive traits to survive in the face of this infectious condition over the past few millennia (Kwiatkowski, 2005).

3.1.2 Fighting the evolution of malaria in Cambodia116 -‐ Berkeley University

July 2012 Malaria117 infects more than 250 million people a year and kills almost one million — most of them children. The disease is curable with the right treatment, but this year scientists announced that it may not be curable for long. Strains of malaria that have evolved resistance to our most effective drug, artemisinin, have been discovered in western Cambodia and could spread to the rest of the world. Understanding the environment that contributed to this worrisome evolutionary step is helping scientists, doctors, and policymakers develop effective strategies for keeping resistant strains of malaria in check. Where's the evolution? At the most basic level, resistance is an evolutionary phenomenon: All populations — including populations of disease pathogens — have genetic variation. Some individuals have the genes to handle particular environmental stresses and opportunities better than others. And when the population is exposed to a stress, the individuals that happen to carry the right mutated genes survive and reproduce at higher rates. Over many generations, individuals carrying the helpful mutations will become more frequent in the population. This is basic natural selection at work, and just as it shapes birds' beaks to take advantage of available seed sizes, it favors the evolution of pathogen populations that can resist the drugs in their environments. Scientists now have evidence that this is exactly what has happened in western Cambodia — and it has them worried for several reasons. First, artemisinin is the most effective malaria drug we have left. The malaria pathogen, Plasmodium falciparum has already evolved resistance to other drugs like chloroquine. Second, Cambodia seems to be a harbinger of malaria resistance. Resistant malaria strains frequently crop up in Cambodia before spreading to the rest of the world. If artemisinin-‐resistant malaria strains become established in Cambodia and then spread, malaria deaths will likely skyrocket.

3.1.3 E. coli caught in the act of evolving118 Following extract from Science News published on Sep 19th, 2012 By Tina Hesman Saey October 20th, 2012; Vol.182 #8 (p. 8) : Wednesday, September 19, 2012

Big leaps in evolution are the products of tiny genetic changes accumulated over thousands of generations, a new study shows.

E. coli bacteria growing in a flask in a lab for nearly 25 years have learned to do something no E. colihas done since the Miocene epoch: eat a chemical called citrate in the presence of oxygen. Evolutionary biologists Zachary Blount and Richard Lenski of Michigan State University in East Lansing and their colleagues describe the molecular steps leading to the feat online September 19 in Nature.

116 Berkeley University – 2012 July 117 Malaria The Scientist – How Blood Cells Thwart Malaria 118 Science News, October 20th, 2012 Nature : Genomic Analysis of a Key innovation in an experimental E. Coli population NCBI – US National Library of Medicine National Institute of Health


The work demonstrates that although new traits seem to emerge in the blink of an eye evolutionarily speaking, those traits are actually the product of thousands of generations of genetic tweaks.

“The ability to be able to not just talk about how genes evolve, but to see it in action is just awesome,” says Bruce Levin, a population and evolutionary biologist at Emory University in Atlanta. “This is really getting at the nitty-‐gritty of evolution.”

Teasing out the molecular details behind the evolution of citrate-‐eating E. colimay help researchers better understand evolution in other organisms.

Learning to eat citrate, also called citric acid, is as big an innovation for E. coli as developing eyes or wings would be for multicellular creatures, says evolutionary geneticist Paul Rainey of Massey University in Auckland, New Zealand, and the Max Planck Institute for Evolutionary Biology in Plön, Germany.

Ancestors of E. coli and other bacteria may once have been able to eat citrate when oxygen is around, but E. coli lost the ability at least 13 million years ago, Blount says. In fact, the inability to grow on citrate in oxygen-‐rich conditions is a defining characteristic of E. coli that helps distinguish them from other types of bacteria.


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3.1.4 Chromosome119 2 in Human DNA120 -‐ Evidence for Common Descent All members of Hominidae except humans have 24 pairs of chromosomes. Humans have only 23 pairs of chromosomes. Human chromosome 2 is widely accepted to be a result of an end-‐to-‐end fusion of two ancestral chromosomes.121

The evidence for this includes:

The correspondence of chromosome 2 to two ape chromosomes (12 & 13). The closest human relative, the chimpanzee, has near-‐identical DNA sequences to human chromosome 2, but they are found in two separate chromosomes. The same is true of the more distant gorilla and orangutan.122

The presence of a vestigial centromere. Normally a chromosome has just one centromere, but in chromosome 2 there are remnants of a second centromere.123

The presence of vestigial telomeres. These are normally found only at the ends of a chromosome, but in chromosome 2 there are additional telomere sequences in the middle.

Chromosome 2 presents very strong evidence in favor of the common descent of humans and other apes. According to researcher J. W. IJdo, "We conclude that the locus cloned in cosmids c8.1 and c29B is the relic of an ancient telomere-‐telomere fusion and marks the point at which two ancestral ape chromosomes fused to give rise to human chromosome 2."

119 Nature (2005) 120 Chromosome 2 – Human : Wikipedia 121 Human Chromosome 2 is a fusion of two ancestral chromosomes by Alec MacAndrew; 18 May 2006. Evidence of Common Ancestry: Human Chromosome 2 (video) 2007 122 Yunis and Prakash; Prakash, O (1982). "The origin of man: a chromosomal pictorial legacy". Science 215 (4539): 1525–1530 Human and Ape Chromosomes; accessed 8 September 2007 123 Avarello et all, (1992). “Evidence of an ancestral alphoid domain on the long arm of human chromosome 2, Human Genetics


3.1.5 Endogenous Retro Virus – Evidence for Common Descent124 Endogenous retroviruses provide yet another example of molecular sequence evidence for universal common descent. Endogenous retroviruses are molecular remnants of a past parasitic viral infection. What makes retroviruses particularly interesting is that they are the only viruses that have the ability to splice foreign genetic elements into the host cell. A retro virus stores its genetic information in RNA and not in DNA. Upon infecting a cell they convert their RNA genome into a DNA through a process called reverse transcription. That DNA then inserts randomly into one of the host’s chromosomes and if the virus happens to infect one of the germ cells (cells that make egg or sperm), then the viral DNA will be passed on to the next generation and all subsequent generations. Occasionally, copies of a retrovirus genome are found in its host's genome, and these retroviral gene copies are called endogenous retroviral sequences. Retroviruses (like the AIDS virus or HTLV1, which causes a form of leukemia) make a DNA copy of their own viral genome and insert it into their host's genome. If this happens to a germ line cell (i.e. the sperm or egg cells) the retroviral DNA will be inherited by descendants of the host. Again, this process is rare and fairly random, so finding retrogenes in identical chromosomal positions of two different species indicates common ancestry.

124 Endogenous Retro Virus – Talk Origins


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3.1.6 Molecular Clocks: Protein Evolution125 Proteins are molecular clocks, and different proteins evolve at different rates. The longer two species have been evolving separately, the more amino acid differences accumulate in the their proteins. Amino acid changes reflect mutations in the genes. The basic mutation rate is probably similar for all genes, but natural selection filters out those mutations that impair a protein’s function. In the course of more than a billion years of evolutionary time, let us look at four proteins that have changed at vary different rates. Histone structure is so rigidly defined for its DNA-‐binding function that in one billion years since plants and animals separated, only one amino acid difference exists between a pea and a cow. On the other hand, Fibrinopeptides can take almost any amino acid change and still carry out their function in blood clotting, and therefore have a fast rate of change. The hourglasses represent time, and the sand grains represent each protein's amino acids. The "clocks" in the upper right were set at zero 90 million years ago, when the fossil record suggests that the major orders of placental mammals diverged from each other, as represented here by the horse and the human. Notice that in the enlarged histone hourglass, none of the sand grains have dropped, showing that in the past 90 million years no amino acid substitutions have occurred in the histones of human and horse.

Histones interact with DNA in the chromosomes, providing structural support and regulating DNA activities such as replication and RNA synthesis. Their ability to bind to DNA depends upon a particular structure and shape. Virtually all mutations impair histone's function, so almost none get through the filter of natural selection. The 103 amino acids in this protein are identical for nearly all plants and animals

125 PBS – Protein Evolution ©2001 WGBH Educational Foundation and Clear Blue Sky Productions, Inc. All rights reserved.


The beta chain of hemoglobin has 146 amino acids; 26 of them differ in horse and human, which is about 18%. Hemoglobin transports oxygen in the red blood cells from the lungs to other tissues throughout the body and so allows an efficient way to use energy. The exact sequence of amino acids is not so important in the hemoglobin molecule as long as it can bind and release oxygen. Because the amino acid substitutions do not interfere with the protein's function, natural selection allows more changes in hemoglobin than in the previous two protein molecules.

Fibrinopeptides are segments of the fibrinogen molecule and have about 20 amino acids. Human and horse amino acids differ in this protein by 86%. Fibrinopeptides are important in blood clotting. The segments simply act as spacers, keeping active sites of fibrinogen apart. When bleeding occurs, the Fibrinopeptides are cut out and discarded, leaving the sticky surfaces free to engage in forming clots. The actual sequence of amino acids is unimportant for this spacer function; so many amino acid substitutions have been tolerated.

Each protein, with its characteristic rate of change, pinpoints the timing of events in different evolutionary time frames. Histones time once-‐in-‐a-‐billion year events. Fibrinopeptides change rapidly, averaging one mutation per million years. Changes within the past five million years between closely related species can be timed with this clock. Biologist Russell Doolittle's Fibrinopeptides sequences in 1970 pointed out the close relationship between chimpanzees and humans, prior to its confirmation in the 1980s.


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3.1.7 Cytochrome126 C It is another classical example to show biochemical evidence for evolution. The primary structure of cytochrome c consists of a chain of about 100 amino acids. Many higher order organisms possess a chain of 104 amino acids. The cytochrome c molecule has been extensively studied for the glimpse it gives into evolutionary biology. Both chicken and turkeys have identical sequence homology (amino acid for amino acid), as do pigs, cows and sheep. Both humans and chimpanzees share the identical molecule, while rhesus monkeys share all but one of the amino acids: Cytochrome c is an enzyme necessary for the oxidation of food, the cell's main chemical reaction for producing energy. Cytochrome c is found in all aerobic (oxygen-‐using) cells, from yeast to multicellular animals. Its vital function limits the changes it can accept.

Following chart is prepared from the info from Richard Dawkins “River out of Eden” book.

126 Cytochrome C – Wikipedia


3.2 Interpreting the Fossil Record

3.2.1 Paleontology It is the study of earlier forms of life present in the fossil record.

3.2.2 Paleoanthropology127 It’s the study of early forms of humans and their primate ancestors. Its focus is documenting and understanding human biological and cultural evolution.

3.2.3 Taphonomy128 It is the study of decaying of organisms (plants, animals, and others) over a period of time and how they become fossilized. Research into these matters shown that fossilization is a rare phenomenon, in order for a fossil to form, the body of the organism must not be eaten or destroyed by erosion and other natural forces. Preservation would mostly occur if the organism were buried quickly and deeply. Organisms with soft bodies like jelly fish, are very uncommon fossils. What most often preserved are hard body parts, such as dense bones, teeth and shells. It is likely that the vast majority of fossils will never be found before they are destroyed by erosion. Even after all these hardships, the large collection of fossils in the museums of all over the world is quite extra ordinary, it is the demonstration of science and extra ordinary hard work by the paleontologists and fossil hunters over the past 200 years.

3.2.4 Doing math with species and fossils Its been estimated that the current living species is around 30 million, i.e., 1% of total (3 billion) species Earth witnessed. Assume for a moment that all the fossils are intact and just waiting to be discovered. Let us do a math now. This is for the creationists who hide behind math! Formula From all over the World fossils found and analyzed per day

fd = 100

Fossils found and analyzed per year fy = fd * 365 = 36,500 Take 1% of the total species ever lived on Earth (1% of 3 billion129)

s = 30,000,000

Time required to find 1% of fossils based on 36,500 fossils per year

tr = s / fy tr = 30 million / 36,500 tr = 821 years

127 Paleoanthropology 128 Taphonomy – Wikipedia 129 Richard Dawkins – River out of Eden


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3.3 Macro Evolution Evidence

3.3.1 Evaluating the Design of Giraffe130 The complexity and intricacy of the bodies of living organisms seems like the epitome of art and science coming together in an explosion of perfection. But that appearance is deceiving, and it has given rise to the popular but erroneous belief that such delicacy must be inevitable result of design and foresight on the part of some Intelligent Designer. The recurrent (inferior) laryngeal nerve (RLN) is a branch of the vagus nerve (tenth cranial nerve) that supplies motor function and sensation to the larynx (voice box). The recurrent (inferior) laryngeal nerve, which branches off the Vagus nerve at the base of the brain, travels down the neck, around the arteries of the heart and travels back up the neck to ennervate the larynx, or voice box, thereby providing motor function.

This path is suboptimal even for humans, but for giraffes it becomes even more suboptimal. Due to the lengths of their necks, the recurrent laryngeal nerve may be up to 4m long (13 ft.), despite its optimal route being a distance of just several inches. The image on the right illustrates this clearly. The required route is from A to B. This is a clear case, which shows that there is no so-‐called “intelligent designer” because the pathway of this nerve is completely illogical — unless, of course, you accept that evolution is the reason for this nerve’s convoluted pathway through the body. 130 Richard Dawkins – Showing the pathway of recurring (inferior) laryngeal nerve


3.3.2 Evolution of Italian Wall Lizards131 In 1971, ten Italian wall lizards (Podarcis sicula) were introduced to the island of Pod Mrčaru from a neighboring island. The lizards were left for decades, and compared to the colony from which they were taken. The wall lizards on Pod Mrčaru, having passed through a tiny genetic bottleneck, were found to have thrived and adapted to their new island. They were found to have shifted from a mainly insectivorous diet to one heavy in vegetation. This diet change seems to have driven dramatic changes in the lizards. The head of the Pod Mrčaru lizards is larger, and has a far greater bite force. These are key adaptations for dealing with chewing leaves. The most exciting sign of evolution is the development of cecal valves, muscles used to separate portions of the intestine. These serve to slow the passage of food through the intestine and give time for the bacteria in the gut to breakdown the plant matter for absorption. This is an entirely novel development in the Italian wall lizard, and a major adaptation.

3.3.3 Evolution of Whales: From Land Animal to the Giant of the Ocean

The nearest ancestors of Earth's largest-‐ever animals were tiny deer like creatures that jumped into rivers to flee prehistoric predators, a new study suggests. These semiaquatic, raccoon-‐size mammals dubbed Indohyus lived in southern Asia some 48 million years ago.

In order to understand the biology of the archaeocetes, it is important to first consider what sort of terrestrial animals cetaceans originally evolved from. For a long time, palaeontologists speculated that whales were in fact close relatives of mesonychians, an extinct group of hoofed carnivores that indeed included the largest terrestrial carnivore (Andrewsarchus) ever. They based this assumption on the rather limited fossil material they had of both the mesonychians and early whales.

131 Wikipedia – Italian Wall Lizards


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But in 1994, Dan Graur and Desmond Higgins, two scientists working on cetacean gene sequences dropped a bombshell. Reviving a claim that had been made as early as the 1950s, they suggested that whales were in fact most closely related to modern artiodctyls. Although further molecular studies supported their results, many scientist were rather reluctant to accept this novel claim and a lively dispute as to whether or not mesonychians should continued to be viewed as the ancestors of whales kept many cetologists busy. But in 2001, a crucial bit of evidence came to light that ended the discussion. One of the most diagnostic features found in the skeleton of artiodactyles is the shape of the astragalus, which somewhat resembles that of a double-‐pulley. Exactely this type of bone, which has never been found associated with mesonychian remains, was found to be part of two archaeocete skeletons. With both molecular and morphological evidence now supporting a cetacean-‐artiodactyl relationship, the traditional order Cetacea was merged with Artiodactyla, thus forming the now widely accepted order Cetartiodactyla. Read more on Whale Evolution from Bristol University, UK… Following data from www.transitionalfossils.com Indohyus ~48 million years ago

Although only a cousin species of the ancestor of whales, Indohyus had bones denser than normal mammals, indicating it was partially aquatic: heavy bones are good ballast (Thewissen et al, 2009). Its ears shared a feature with modern whales: a thickened wall of bone which assists in underwater hearing; non-‐cetaceans don't have this (Thewissen et al, 2009).

Pakicetus ~52 mya Perhaps the actual ancestor, Pakicetus was probably semi-‐aquatic; like Indohyus, it had dense bones for ballast (Thewissen et al, 2009). Its body was "wolf-‐like" but the skull had eye sockets adapted for looking upwards, presumably at objects floating above it (Thewissen et al, 2009). Although initially known from just a skull, many more bones were found later (Thewissen et al, 2001).

Ambulocetus ~50 mya With a streamlined, elongated skull and reduced limbs, Ambulocetus probably spent most of its time in shallow water. Its reduced limbs meant it could only waddle on land (Coyne, 2009). It resembled a crocodile in some ways.

Rodhocetus ~45 mya The nostrils of Rodhocetus have started to move backwards (towards the blowhole position) and the skeleton indicates a much stronger swimmer (Coyne, 2009). On land it would struggle, moving "somewhat like a modern eared seal or sea lion" (Gingerich et al, 2001). Its teeth were simpler than its predecessors (Futuyma, 2005), a trend that continued to the present.

Maiacetus ~47 mya Seems similar to Rodhocetus. One fossil was found with what appeared to be a foetus, in a position indicating head-‐first birth (Gingerich et al, 2009) unlike modern whales. However this is disputed; the "foetus" might just be a partially digested meal (Thewissen and McLellan, 2009).

Basilosaurus ~40 mya


The whale-‐like, fully aquatic Basilosaurus had almost lost its (tiny) hindlimbs, but they had not yet vanished entirely (Prothero, 2007).

Dorudon ~40 mya Also fully aquatic, Dorudon also had tiny hind limbs, which "barely projected from the body" (Futuyma, 2005).

Aetiocetus ~25 mya The blowhole in Aetiocetus is about halfway to its position in modern whales on top of the head. Aetiocetus also represents the transition from toothed whales to the filter-‐feedingbaleen whales, being similar to baleen whales in most respects, but possessing teeth (Van Valen, 1968).

From Land to Water: the Origin of Whales, Dolphins, and Porpoises132 • J. G. M. Thewissen, Northeastern Ohio Universities College of Medicine, USA • Lisa Noelle Cooper, Northeastern Ohio Universities College of Medicine, USA • John C. George, Department of Wildlife Management, AK, USA • Sunil Bajpai IIT Roorkee, India Whales evolved relatively quickly. As Coyne (2009) explains, "adapting to life at sea did not require the evolution of any brand-‐new features -‐ only modifications of old ones". Thewissen et Cooper, George & Bajpai (2009) give a good overview of whale evolution, which is freely available. Articles on Whale Evolution 1. Bristol University - Whale Evolution

2. Berkeley University - Whale Evolution

3. BBC News - Whale Evolution

4. Discovery Science - Whale Time Line

5. National Geographic - Whale Evolution

6. Smithsonian - Whale Evolution

7. PBS - Whale Evolution

8. IIT Roorkee - Evolution of Whale - By Bajpai, Thewissen, Sahni

9. Talk Origins - Whale Evolution

10. BBC Prehistoric Life

11. WHO Children mortality Rate

Videos on Whale Evolution

1. Nature - Whale Evolution

2. National Geographic - Whale Evolution

132 Springer Link – http://link.springer.com/article/10.1007%2Fs12052-‐009-‐0135-‐2


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Creationist Answers to Whale Evolution 1. Creation Ministries - Refuting Evolution

2. DarwinismRefuted.com - Myth of the Walking Whale


3.4 Transitional Fossils One of the key arguments for creationists for more than a century is to ask the question – “where are all the transitional fossils to describe common descent?” On February 12th, 2009, 200th birthday of Charles Darwin, National Geographic133 asked prominent scientists to pick up critical transitional fossils. Transitional fossil shows an in between species, species which has features of two different species. For example if fish evolved into a land animal, then a transitional fossil between fish and land animal should share features of both the species. Following are the 7 Key fossils presented in National Geographic Key Transitional Fossil Significance of this fossil 1. Tiktaalik – Found in Artic Canada in

2004, 375 million years old. Tiktaalik is a key fossil when the aquatic ancestors started their journey towards land. This is the key link for Fish to Tetrapods

2. Archaepteryx – Found in Germany in 1861, 150-‐145 million years old.

Found 2 years after publication of Origin of Species, this species shares features with both meat-‐eating dinosaurs, in the wrist, snout, tail, and pelvis and birds, such as asymmetrical, vanned feathers and very long feathered wings.

3. Amphistium – Found in 2008, 50 million years old.

The fossils flatfish eyes are not quite on opposite sides of its body and note quite in their modern asymmetrical arrangement.

4. Ambulocetus – Found in Pakistan in 1992, 50 million years old.

This fossil shows something with a whale’s head, the beginnings of an aquatic lifestyle with webbed hands and feet, but still fully quadrupedal.

5. Homo Ergaster – Found in 1984 in Kenya, 1.6 million years old

Fred Spoor of University College London said that, whereas fossils of our earliest human ancestors "can very much be seen as apes who adopted a bipedal gait," Turkana Boy "is a true intermediate between modern humans and other primates."

6. Hyracotherium / Eohippus – Fox like horse found in US 1867, 55 million years old.

There was no hard evidence to show how an existing animal had evolved from prehistoric species—until Hyracotherium, kicked off a series of fossil discoveries depicting the evolution of horses over 55 million years. Paul Sereno of the University of Chicago says Hyracotherium/Eohippus is up there historically with Archaeopteryx. The paleontologist named Eoraptor—the small transitional dinosaur at the root of the dinosaur family tree—with Eohippusin mind.

7. Thrinaxodon – Fossils from S. Africa and Antarctica, 245 million years old.

A perfect intermediate between reptiles and mammals. It was a cat size burrower that had scales and laid eggs. But like mammals, it had whiskers, warm blood.

133 National Geographic – 7 Missing links since Darwin


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3.4.1 Tiktaalik134: Fish to Tetrapods (Amphibians, Reptiles, Mammals) Transition Fossil – Tiktaalik discovered in 2004 in Artic. Following extract is from PBS Nova135 web site

Eusthenopteron looked and behaved a lot like modern fish, but hidden within its fins were the precursors of the arm and leg bones of four-‐limbed land animals. The later Tiktaalik took a further step toward terrestrial life with early wrist and finger bones that allowed the animal to prop itself up and poke its head from the water of the shallow swamps it favored. Tiktaalik's skeleton indicates that it probably breathed both through gills, like Eusthenopteron, and through a lung-‐like structure, like the laterIchthyostega and modern amphibians. Ichthyostega's even stronger limbs probably developed so that it could maneuver around thick vegetation in its marshy habitat and even haul itself along muddy banks when necessary.

Image not to the scale

134 Tiktaalik – Wikipedia 135 PBS Nova -‐ http://www.pbs.org/wgbh/nova/id/tran-‐nf.html


3.4.2 Thrinaxodon136 : Reptiles to Mammals Following extract from PBS Nova137 web site

Despite its distinctly lizard-‐like appearance, Dimetrodon possessed a suite of traits more common to later mammals than to its close relatives, the true reptiles. Most notably, the sail protruding from Dimetrodon's back allowed the animal to partially regulate its body temperature, marking what could have been a major point in the transition to warm-‐bloodedness. The later Thrinaxodon didn't have a sail but was probably covered in fur and might have been warm-‐blooded like the early mammal Morganucodon. Another documented shift toward mammals took place in the mouth: Dimetrodon had differentiated teeth and a strong bite, although it gulped its prey whole like true reptiles do even today. Thrinaxodon developed a stronger lower jaw and could chew, but it was Morganucodon that sported both sharp teeth and grinding molars like we have today. Image not to the scale

136 Thrinaxodon -‐ Wikipedia 137 PBS Nova -‐ http://www.pbs.org/wgbh/nova/id/tran-‐nf.html


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3.4.3 Archaeopteryx138 : Reptiles To Birds Following extract from PBS Nova139 web site

Few topics spark as much controversy among paleontologists as the transition from reptiles to birds. Experts don't know what Archaeopteryx's closest dinosaur ancestor looked like—fossils haven't yet been found—but they think it might have looked somewhat like Velociraptor (hence our showing it here, despite its much later age). Archaeopteryx, the first known bird, did share a common ancestor with Velociraptor as well as traits this ancestor would have had: sharp claws for grasping prey and long hind legs and a stabilizing tail for running, for example. Yet Archaeopteryx also had feathers indicative of early flight, although the orientation of its shoulder joint and its lack of a bony breastbone imply the animal was more of a glider than many modern birds—it couldn't lift its wings above its back or flap them for extended flight. Archaeopteryx's later bird relative, Yanornis, had a bone structure more conducive to bird flight as we know it today. It could flap its wings and, like many modern birds, it had a short, aerodynamic tail. Like Archaeopteryx, however, Yanornis did retain some dinosaurian features, including teeth. Image not to scale

138 Archaeopteryx – Wikipedia 139 PBS Nova -‐ http://www.pbs.org/wgbh/nova/id/tran-‐nf.html


3.4.4 Ambulocetus140 : Land Mammals To Ocean Giant Following extract from PBS Nova141 web site

Pakicetus may have looked somewhat like a dog with hoofs, but it was actually an early cetacean—a group that comprises the dolphins, porpoises, and whales. The proof, scientists say, lies in Pakicetus's ears, which were intermediate between those of terrestrial and fully aquatic mammals, and in its triangular, whale-‐like teeth. Pakicetus and its relatives were possibly fish-‐eating scavengers that ventured into the water to find live prey. Although the later Ambulocetus had tiny hoofs on its hind legs and could probably walk, its toes were webbed like those of modern mammals adapted for swimming. Its fossilized bones suggest that Ambulocetus undulated its spine vertically in the water like the still later Basilosaurus (as well as modern otters and whales) and not side-‐to-‐side like fish. Although Basilosaurus had tiny, weak hind "legs" left over from its evolutionary past, the animal was probably fully aquatic. Its sturdy front flippers were particularly adapted for the water, though they still had an arm-‐like bone structure as in those of modern cetaceans.

Image not to the scale

140 Ambulocetus – Wikipedia 141 PBS Nova -‐ http://www.pbs.org/wgbh/nova/id/tran-‐nf.html


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3.4.5 Quadrupedal Primates to Bipedal Primates The most hotly debated and controversial subject for creationist is to accept that Humans are evolved from Ape. That’s completely against the belief of Abrahamic religions, which says that Humans are created in the image of God. The fact remains there were atleast half a dozen human species lived in this planet and there was a time atleast 2-‐3 human species lived together. When I say human species, I mean species like Homo sapiens with following features

1. Had a spoken language 2. Engaged in Cave arts and sports 3. Cooked their food 4. Buried the dead body of fellow humans

Now its time we need to look at the different groups of Humans. Following images from Smithsonian Museum:

This is the latest finding based on the fossil evidence. The above fossils clearly show that we (Homo Sapiens) were not the only intelligent species on this planet. Unfortunately due to various circumstances rest of the intelligent species got wiped out. One theory says we might be the reason for wiping out Neanderthal’s. Let us first take a look at the first group that’s the Homo Group and figure out different species in that.


Following image zooms in to the Homo Group first. Homo Group

Paranthropus Group

Astralopithacus Group

Ardipithecus Group

Following extract from PBS Nova142 web site

The early ape Dryopithecus was probably a common ancestor to humans and the other great apes. Although Dryopithecus lived mainly in trees, fossil evidence shows that the animal walked on all fours whenever it descended to

142 PBS Nova -‐ http://www.pbs.org/wgbh/nova/id/tran-‐nf.html


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the forest floor. In fact, humans' more recent ancestor, Australopithecus afarensis, retained some remnants from its quadrupedal past, such as hind toes suited for climbing and a wrist joint indicating it sometimes knuckle-‐walked. But Australopithecus probably stood upright most of the time: Its femur was shaped similarly to that of the later Homo erectus and could bear the stress of habitual upright movement. Both protohumans' femurs were also angled inward to an almost knock-‐kneed position. This helped Australopithecus and H. erectus maintain their balance on two legs, just like we do today.


3.5 Final nail in the coffin of the creationists

3.5.1 Three stages of Evolutionary Biology

1. Charles Darwin – Natural Selection 2. Modern Synthesis 3. Evo Devo – Evolutionary Developmental Biology

Most of the time creationist’s arguments revolve around missing fossils. This is an irrational argument as every new fossil discovered is enhancing the evidence supporting Evolution, because no fossil till to date went against the Geological time line. If Evolution is wrong it’s much easy to find fossils all over the geological time line without any logic or common sense. Another misconception by creationists is that, a new scientific theory eliminates old scientific theory. The best examples of these are misinterpretation of Stephen Gould’s Punctuated Equilibrium and Genetic Science. Natural selection is a very critical part on both theories.


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3.5.2 Creationists buried for ever The most exciting thing about evolution is the synchronization of the data between completely three different domains as follows:

1. Earth’s Geological Time Line (4.5 years of History) 2. Fossil records starting from 3.5 billions years to current 3. Molecular clocks (Evolution of proteins)

When you combine the above three data sets together it clearly shows the pattern on gradual evolution (in geological time frame). Consider the following table on fossil record.

Type Bacteria143 Jelly Fish144 Fish145 Amphibians146 Reptiles147 Mammals148 24 hour Time Scale 8:48 pm 9:00 pm 10:00 pm 10:45 pm 11:40 pm Fossil Record 3.4 bya 530+ mya 530 mya 397149 mya 340 mya 195 mya

Now compare this with Geological time line and the Molecular clocks. The case is closed.

143 Discovery Channel: Oldest fossil of bacteria, living 3.4 billion years were found in Australia 144 National Geographic: Oldest Jelly Fish fossil record, half a billion years 145 BBC News: Oldest fish fossil record 530 million years ago 146 Berkeley University: Oldest Amphibian fossil record 368 million years 147 New York Times: Oldest Reptile fossil record 340 million years 148 Harvard University: Oldest Mammal fossil record 195 million years 149 National Geographic – Oldest land walker tracks found Jan 6, 2010


4. Conclusion

4.1 Summarizing the critical mistakes from the article The mistakes by Hussain in the first chapter of his Evolution and Genetic Science series:

1. Not describing the basic concepts of Darwinism. For Hussain, Darwinism is nothing but Natural Selection with a linear gradual selection. He doesn’t talk about Common Descent and Single Origin of Life.

2. Hussain quotes lot of Scientists (Evolutionist) who turned as Anti Evolutionist because of the failure of Darwin’s evolution theory, in reality it turned out to be Hussain’s failure in understanding the writings of those scientists.

3. Hussain’s lack of understanding of Punctuated Equilibrium Theory proposed by Stephen Gould, Niles Eldredge.

4. Hussain’s lack of understanding of Neutral Theory of Molecular Evolution proposed by Motoo Kimura.

5. The worst part is twisting the theories completely out of context and incorrectly to support Hussain’s own version of creationism!

6. There is something even more worse is, Hussain’s lack of understanding of Darwin’s theory itself. Hussain emphasize that Natural Selection is a linear process, where Darwin himself stated it’s NOT necessarily a linear process.

7. As per Hussain, Darwin’s theory is only Natural Section, however, if you study deeply you will understand that “On Origin of Species” is a collection of very profound and insightful theories to understand the Evolution of the Species.

8. These conclusions prove that Hussain is an ardent fan of creationism, which is nothing but faith, which is a strong belief in God or in the doctrines of a religion, based on spiritual apprehension rather than proof.

Evidence provided in this document is a tip of the iceberg150 , Hussain will have a hard time to refute all these evidence from micro and macro world. I never expected someone would go to such a length (misquoting scientists, twisting the new theories) to prove creationism! Like I said before, you don’t need to prove or disprove anything to hold your faith (faith in God). Creationist feasts like a cunning wolf when there is a controversy on any scientific evidence. The best example of this the case of IDA151 fossil (it moved under Lemur branch). If we have to go through all the evidences collected in the last 150 years, a room full of shelves will not be good enough to keep the books on empirical data supporting Evolution.

150 R. Dawkins – The Ancestors Tale, The blind Watchmaker, Selfish Gene, Climbing Mount Improbable Sean Caroll – The making of the Fittest, Endless Forms Most Beautiful 151 IDA Fossil – Wikipedia New Scientist – Why IDA is not the missing link. May, 2009 PLOS – Complete Primate skeleton, Morphology and Paleobiology (IDA)


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4.2 Analyze Creationism, Intelligent Design and Evolution

4.2.1 Analyzing the Micro and Macro Evidence

1. The recurrent (inferior) laryngeal nerve of Giraffe is a classic case of terribly bad design. Even a bad human engineer will not think about such a bad design. There is another similar bad design in the male anatomy of many vertebrates.

2. The fight between Humans and Malaria is a classic case of Natural Selection. It’s a case at the molecular level. Hussain, made fun of the imaginary examples of Darwin’s wolf case (which talks about the pressure to survive will leads to natural selection and gets better in surviving), and asserted that we don’t see any such evidence right in front of our eyes. The case of survival fight between Humans and Malaria (for the last 100,000 years) is classic case of Natural Selection and arms race between two species.

3. Natural selection picks up the mutation, which is beneficial for the current crisis the species is facing. Even if that mutation solves the current crisis, it can be potentially harmful in the future. Which shows that Natural Selection doesn’t do long term planning something a designer keeps in mind when the designer designs something. The classic example is the Sickle Cell mutation to combat malaria by the Humans. However, we know that inheriting sickle cell from both parents is fatal.

4. Transitional fossils and Genetic evidences shows spectacular evidence in the evolution of Whales, which is an astonishing story of a land mammal similar to a wolf, evolving into the giant of the ocean. Of course, its unbelievable, truth is stranger than fiction.

4.2.2 Analyzing Intelligent Design

1. Fossil records shows appearance and disappearance of species especially when they branch of into a new species. Applying this fossil record on Intelligent Design, it looks like the designer start with some species and then realized that it cant adapt to the new environment (I assume even the environment also is designed by the Intelligent Designer), so the Designer does some modifications so that a new species arise while the less adaptable species vanishes (destroyed by the designer). This is something like a trial and error method the designer is doing for the past 3 billion years in the history of planet Earth. In software industry, a designer like this will be known as a very bad programmer/designer.

2. The fundamental concept of Intelligent Design is, some things are so beautiful in its design (which means we don’t understand its workings or origins), has to be designed. Just because we don’t understand something now doesn’t mean that we can replace that with a much more complex entity (Designer). How will you ever figure out the internal structure, workings of a designer? Oh, you are not supposed to ask such questions.

3. By applying the above logic, how can there be bad designs? The best example is the case of the recurrent (inferior) laryngeal nerve of Giraffe. That’s one of the worst designs. So, does it mean that the same designer created such a


worse design too? Or does it mean there were two designers? One creates good design and the other one creates bad designs?

4. Intelligent design is creationism under a new umbrella, masquerading as Science. Intelligent design proponents pretend to be sleeping when they encounter bad design. They can only see design, which looks good in their eyes and ignores the concept that they are replacing something complex with something exponentially complex (Designer).

5. If you want break evolution just find one fossil, which will destroy the evolutionary time line. Just one that’s all it required.

4.2.3 Analyzing Creationism

1. Creationism is a pure religious concept. There will be inaccuracies in the description of creationism in various religious texts because none of these are authentic scientific analysis, and the purpose of these religious texts are not to give a scientific explanation to the workings of the nature.

2. Believing in these texts are by pure faith rather than questioning such faith. 3. Faith is strong belief in God or in the doctrines of a religion, based on spiritual

apprehension rather than proof. 4. Science and religion simply deal with different realms. Science deals with

natural causes for natural phenomena, while religion deals with beliefs that are beyond the natural world, that’s why in religion it’s OK to invoke Super Natural powers to solve complex issues. In science, the moment you invoke Super Natural powers then its NOT science anymore!

5. If you want break evolution just find one fossil, which will destroy the evolutionary time line. Just one that’s all it required.

4.2.4 Questions to Creationists and Intelligent Design Proponents

1. How do you explain bad design, does it mean there is a bad designer? 2. How do you explain Chromosome 2 or ERV in Human DNA? 3. How do you explain the History of Earth along with fossil record with the

extinction of species? 4. How do you explain the extinction of Dinosaurs and the very late entry of

Humans? The intelligent Designer did that, so that the Designer can bring in Humans?

5. How do you explain 3-‐4 different species of Intelligent Humans lived at the same time, of course on planet Earth?

6. Do you expect other habitable planets (like Earth) in this Galaxy? 7. If there are habitable planets, then do you expect intelligent life forms on

those planets? 8. If there are intelligent life forms on those planets, do you expect them to

have a religion? 9. What’s your theory on how Earth formed and Origin of species on Earth?


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If you have only ONE answer to all the above questions is, its Gods plan, then my answer to you is, thank you, I will have that (Creationism or Intelligent Design concept) in a religious place rather than in a classroom. Classrooms are meant ONLY for science (even an arts or sports student need to learn the basic math). Else If your answer is religion is not suppose to answer any of these questions because it’s beyond human comprehension to understand the purpose of God, then I agree that as long as it’s in the realm of Faith and stays there. However, when you masquerade Intelligent Design as a Science then, people with curious mind will like to know how the nature behave in a certain fashion and why it behaves like that (I am not asking for a purpose, because that’s a human construct). So, to sum it up, Science has a job to do, to unravel the mysteries of the nature and that’s NOT the job of religion.

4.2.5 Some more interesting questions to creationists of Abrahamic faith. If you take all the holy books of three Abrahamic religions (Jews, Christians and Muslims), it talks about a great flood and Noah’s ark. To save all the species, God asked Noah to take two of every species into the Ark. The problem starts when you do literal interpretation of the text. Here are some interesting questions based on the Flood, Ark and Earth.

1. If God asked Noah to take two of every species, so that they can survive, why do we see so many extinct species fossils (99% of the species ever lived were already extinct)?

2. What explanation do the creationists have on extinction of species? Until recent time they never accepted the concept of species extinction.

3. According to both Holy Bible and Holy Qur’an the Earth is created in 6 days. Is this right?

According to N M Hussain Big Bang is a myth, and contribution of modern science is nothing but dreaded diseases like cancer. Here is Human population chart for the last 500,000 years. Checkout the last 500 years and see how the population exploded after scientific revolution.


5. Explore (Videos and Books)

5.1 Glossary Adaptation -‐ A genetically controlled trait that increases an individual's fitness. Alleles -‐ Variations of a given gene. Balanced Polymorphism -‐ A situation in which it is beneficial for a population to maintain two different alleles creating different phenotypes within the population. DNA -‐ Abbreviation for deoxyribonucleic acid, the genetic material of most organisms. Fitness -‐ The probability that an individual will contribute its genes to the next generation Gene pools -‐ All of the genes of all of the individuals in a population make up a gene pool. Genotype -‐ The genetic make-‐up of an individual. Compare with phenotype. Heterozygote Advantage -‐ A situation in which a single disadvantageous allele is not selected out of a population, because, when a person is heterozygous for that allele (the person has one disadvantageous allele and one normal allele), the person gains some sort of local advantage by having the disadvantageous allele. For example, the allele for sickle-‐cell anemia offers resistance to malaria. If a person in an area high in malaria is heterozygous for sickle-‐cell anemia, the resistance they gain to malaria outweighs the disadvantage of having heterozygous sickle-‐cell anemia. A person with two sickle-‐cell anemia cells in such a region is will not have a greater advantage, even if they are completely resistant to malaria. What's the use of being resistant to malaria if you're blood can't carry oxygen? Independent assortment -‐ The inheritance of different genes independently of each other. Lamarckism -‐ The theory of evolution stating that species change over time and that this change occurs through use and disuse and the inheritance of acquired traits. Modern synthesis -‐ Also called Neo-‐Darwinism and the synthetic theory of evolution, the theory of evolution that combines Darwinism with information gained from modern experimental geneticists, population biologists, mathematicians, and paleontologists. Mitosis – It is a process of nuclear division in eukaryotic cells that occurs when a parent cell divides to produce two identical daughter cells Natural Selection -‐ The theory holding that competition exists within species, determining which species live to have offspring and pass their traits on to those offspring. Phenotype -‐ The traits or characteristics an individual displays. Compare with genotype. Polygenic -‐ A phenotype that is controlled by more than one gene is said to be polygenic Populations -‐ A group of genetically similar individuals that live in the same area and usually interbreed. Recombination -‐ The rearrangement of genes on a chromosome that takes place during sexual reproduction. Speciation -‐ The creation of a new species.


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5.2 Videos

5.2.1 Evolution and Genetics

1. Howard Hughes Medical Institute152: 2011 Holiday Lectures – Bones, Stones and Genes. The Origin of Modern Humans

a. Lecture 1: Human Evolution and the Nature of Science, By Tim D. White, Ph. D.

b. Lecture 2: Genetics of Human Origins and Adaptation, By Sarah A. Tishkoff, Ph. D.

c. Lecture 3: Stone Tools and the Evolution of Human Behavior, By John J. Shea, Ph. D.

d. Lecture 4: Hominid Paleobiology, By Tim D. White, Ph. D. 2. Howard Hughes Medical Institute153: 2006

a. Fossil, Genes and Mousetraps, By Kenneth Miller, Ph. D. 3. Howard Hughes Medical Institute154: 2005 Holiday Lectures – Evolution:

Constant Change and Common Threads a. Lecture 1: Endless Forms Most Beautiful, By Sean B. Caroll, Ph. D. b. Lecture 2: Selection in Action, By David M. Kingsley, Ph. D. c. Lecture 3: Fossils, Genes, and Embryos, By David M. Kingsley, Ph. D. d. Lecture 4: From Butterflies to Humans, By Sean B. Caroll, Ph. D.

5.3 Websites on Evolution

5.3.1 Universities

1. Berkeley University – Evolution 101, Understanding Evolution 2. Harvard University – Evolutionary Developmental Biology 3. MIT – Evolution of the Immune System 4. University of Utah – Learn Genetics 5. University of Utah – Variation, Selection and Time

a. Recipe for Evolution: Variation, Selection & Time b. Evolution Starts with DNA c. Evolution in Action d. Change over Time

5.3.2 Web Sites

1. PBS Web Site: http://www.pbs.org/wgbh/evolution/ 2. New Scientist: http://www.newscientist.com/topic/evolution 3. Trust Sanger Institute – Human Genome Project 4. Nature – Genetics: http://www.nature.com/scitable/topic/genetics-‐5 5. Nature – Evolutionary Genetics:

http://www.nature.com/scitable/topic/evolutionary-‐genetics-‐13 152 HHMI -‐ http://www.hhmi.org/biointeractive/evolution/lectures.html 153 HHMI -‐ http://www.hhmi.org/biointeractive/evolution/lectures.html 154 HHMI -‐ http://www.hhmi.org/biointeractive/evolution/lectures.html


5.4 Books

5.4.1 Cosmology and Quantum Physics

1. A Brief History of Time, Stephen Hawking 2. The Grand Design, Stephen Hawking 3. The Elegant Universe, Brian Greene 4. The Fabric of the Cosmos, Brian Greene 5. The 4% Universe, Richard Panek 6. The Holographic Universe, Michael Talbot 7. Parallel Universe, Michio Kaku 8. Hyperspace, Michio Kaku 9. A Universe from Nothing, Laurence M Krauss 10. The inflationary universe, Alan Guth 11. The Tao of Physics, Fritjof Capra 12. Massive, The hunt for God Particle, Ian Sample

5.4.2 Evolution and Genetics

1. Endless Forms Most Beautiful, Sean B Caroll 2. The making of the Fittest, Sean B Caroll 3. The Greatest show on Earth, Richard Dawkins 4. The Blind Watchmaker, Richard Dawkins 5. The Selfish Gene, Richard Dawkins 6. Climbing Mount Improbable, Richard Dawkins 7. The Ancestors Tale, Richard Dawkins 8. The River out of Eden, Richard Dawkins 9. On Origin of Species, Charles Darwin 10. Acquiring Genomes, Lynn Margulis & Dorion Sagan 11. Genetics and the Origin of the Species, Theodosius Dobzhansky 12. Modern Synthesis, Julian Huxley 13. Punctuated Equilibria, Stephen Jay Gould 14. Edge of Evolution, Michael Behe 15. Darwin’s Black Box, Michael Behe

5.4.3 Neuro Science

1. The phantoms in brain, V S Ramachandran 2. Tell a Tale Brain, V S Ramachandran 3. Free Will, Sam Harris

5.4.4 Others

1. The God Delusion, Richard Dawkins 2. The Moral Landscape, Sam Harris 3. Why I am not a Christian? Bertrand Russell 4. Religion and Science, Bertrand Russell