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Atheism – a quick reference flash guide


         This page is meant to serve as a quick reference to topics surrounding atheism, theism, science, evolution and creationism.


NB References are given in the brief format, indicating the PubMed ID, which starts “PMID:”. Simply follow the link or type the PubMed ID into PubMed at:


EA, 10.2009



Flash FAQ... 1

General.. 1

What is meant by “God” or “gods”?. 1

What is atheism?. 2

Is it possible to be atheist and agnostic?. 2

Is evolution incompatible with the belief in God?. 2

Physics.. 3

Can the “fine-tuning” of fundamental physical constants in our universe be explained naturally?  3

Biology.. 3

Did we have blood or a heart first?. 3

When we came out of the ocean, did we have gills or lungs?. 3

Did we have a skull or a brain first?. 3

Did we have one arm before we had two? Did we have legs or arms first? Why don’t we have 3 arms?  3

Why did sexual reproduction evolve?. 4

Can the origin of life be explained naturally?. 4

Proof of evolution and prebiotic abiogenesis.. 4

1.      The fossil record combined with dating methods shows a radiating pattern of life in a tree-like fashion. Transitional forms are documented in the fossil record.  4

2.      DNA evidence suggests common ancestry and the same radiating pattern as the fossil record.  5

3.      Endogenous Retroviruses (ERVs) scattered in vertebrate genomes also show a clear radiating pattern of common ancestry. This is best explained with evolution.  5

4.      Speciation has been observed experimentally.. 5

5.      Beneficial mutations have been observed experimentally.. 5

6.      Abiogenesis has been supported by experimental evidence.. 6

7.      Synthetic cells have nearly been synthesised.. 7

Intelligent design (ID) debunked... 7

Complex-specified information (CSI). 7

Irreducible complexity.. 9

The “bacterial flagellum”. 9

The eye.. 9

Others. 10

According to a literal interpretation of the Bible, God is evil.. 10

Literal interpretations of some passages of the Qur’an and the Hadith can motivate fundamentalist behaviour   11

The Bible is scientifically incorrect.. 12

Destructive impact of Abrahamic religions.. 13

Atheism is a more healthy belief system than Abrahamic religion.. 14

1.      Atheism correlates positively with IQ.. 14

2.      Only about 7 % of leading scientists in the US believe in God. This probably even lower in Europe.  14

3.      Atheist countries do better in indicators of social welfare.. 14

4.      Atheists have a higher education level in the USA.. 15

5.      In the USA, church attendance by state positively correlates with property crime (Burglary, Larceny-theft, Motor vehicle theft) significantly.  15

General links to primers and resources.. 15

Physics and cosmology.. 15

Articles/sites:. 15

Videos:. 16

Evolution.. 16

Articles/sites:. 16

Videos:. 17





Flash FAQ




What is meant by “God” or “gods”?

         Usually, “God” is defined as follows.







1. A being conceived as the perfect, omnipotent, omniscient originator and ruler of the universe, the principal object of faith and worship in monotheistic religions.

2. The force, effect, or a manifestation or aspect of this being.



A being of supernatural powers or attributes, believed in and worshiped by a people, especially a male deity thought to control some part of nature or reality.



The American Heritage® Dictionary of the English Language, Fourth Edition



What is atheism?

         Atheism is the lack of belief in a God or gods. Ideally, it should be specific to a particular God, but in common everyday language, the God in question is usually the Abrahamic God. Loosely speaking, therefore, unless specified otherwise, atheism refers to atheism with respect to the Abrahamic God.


         Another acceptable definition, proposed by Hitchens and others, is as follows:


“The atheist says no persuasive argument for the existence of God has ever been advanced or adduced without convincing rebuttal.”


Hitchens: deism, theism, wishful thinking.


Is it possible to be atheist and agnostic?

         Yes. Agnosticism means that you think the concept of God is inherently impossible to prove or disprove, or that you simply don’t know if God exists or does not exist with absolute certainty. Atheism allows for the belief that God is very unlikely and probably does not exist, while still maintaining that there is a very small chance he does exist.


Is evolution incompatible with the belief in God?

         In my opinion, yes. However, some distinguished biologists, namely Ken Miller and Francis Collins argue otherwise. Both of them have used the anthropic principle as an argument for God but omitted the explanation for the fine-tuning of fundamental physical constants provided by multiverse interpretations of the latest unified theories in physics such as string theory and loop quantum gravity. Miller also brings forth the uncertainty elements in quantum mechanics as a leeway for free will in humans and this position has been criticized by other scientists. Francis Collins argues that this uncertainty in the quantum mechanical world provides way for God to intervene in the world, thus allowing directed evolution by God. Again, this position has been criticized by other scientists.


Quantum arguments for God veer into mumbo-jumbo






Can the “fine-tuning” of fundamental physical constants in our universe be explained naturally?

         Yes. There are interpretations of quantum gravity theories in physics that allow anthropic selection of universes with observer bias such that some of the fundamental constants are restricted, in particular the cosmological constant. See links below.






Did we have blood or a heart first?

         Blood came first. Early organisms did not need a heart to pump the fluid that contained nutrients around their body.


When we came out of the ocean, did we have gills or lungs?

         Gills came first. Transitional form between fish and land animals had a transitory apparatus that allowed them to take little gasps of air outside the water for short periods of time.


How Fish Jumped out of the Water: Evolution of the Lung



Did we have a skull or a brain first?

         Brains came first. Early organisms had very rudimentary brains and then they got larger and more complex. Then it became encased by a skull in some vertebrate lineages, providing extra protection.


Did we have one arm before we had two? Did we have legs or arms first? Why don’t we have 3 arms?

         No. Limbs developed symmetrically from symmetric fins on early fish. We first had four legs then 2 of the 4 legs became arms in the early hominid lineages.


Why did sexual reproduction evolve?

         During the origin of eukaryotic cells, when mitochondria were engulfed by the host cells, the host genome was bombarded by bacterial introns and increased mutation rate. So sex was the only mechanism that helped survival because it improved the efficiency of selection, allowing good genes to recombine away from the junk residing in the genetic backgrounds. That is the origin of sexual reproduction. It happened quite early at the eukaryote lineage.


Can the origin of life be explained naturally?

         Yes. See links below.





Proof of evolution and prebiotic abiogenesis


1.  The fossil record combined with dating methods shows a radiating pattern of life in a tree-like fashion. Transitional forms are documented in the fossil record.


Original Lucy paper:


Johanson DC et al. Plio--Pleistocene hominid dis...[PMID: 815823]


Franzen JL et al. Complete primate skeleton fro...[PMID: 19492084]


Gibbons A. Ardipithecus ramidus. A new k...[PMID: 19797636]


List of transitional fossils




2.  DNA evidence suggests common ancestry and the same radiating pattern as the fossil record.


Marques-Bonet T et al. Sequencing primate genomes: w...[PMID: 19630567]


Interactive Tree Of Life




3.  Endogenous Retroviruses (ERVs) scattered in vertebrate genomes also show a clear radiating pattern of common ancestry. This is best explained with evolution.


Oliver KR et al. Transposable elements: powerf...[PMID: 19415638]




4.  Speciation has been observed experimentally.


Schluter D. Evidence for ecological speci...[PMID: 19197053]


Observed Instances of Speciation




5.  Beneficial mutations have been observed experimentally.


Mutations found in people which make them accumulate less “bad” cholesterol and therefore are less likely to suffer from circulatory disease:


Groenemeijer BE et al. Genetic variant showing a pos...[PMID: 9193431]


A mutation in people that makes a G-protein cascade work better and therefore gives a better immune system:


Virchow S et al. Enhanced fMLP-stimulated chem...[PMID: 9781669]


10 adaptive mutations found in bacteriophages that make them more resistant to high temperatures:


Knies JL et al. The genetic basis of thermal ...[PMID: 16732695]


A mutation in Yeast in the enzyme acid monophosphatase that made it better at metabolising/3-glycerophosphate:


Hansche PE. Gene duplication as a mechani...[PMID: 236976]


Mutations in bacteria that make them grow faster and better:


Papadopoulos D et al. Genomic evolution during a 10...[PMID: 10097119]




6.  Abiogenesis has been supported by experimental evidence.


         The origin of life and formation of the first cells is dealt with in a field called abiogenesis. It is a theory separate from evolution. The first cells were either RNA replicases enveloped in a fatty acid bilayer or proteinaceous membranes with co-evolving RNA and protein. The formation of RNA has been demonstrated experimentally under prebiotic conditions. In other words, there is experimental proof that even under the early Earth’s conditions, RNA can form.


Powner MW et al. Synthesis of activated pyrimi...[PMID: 19444213]


Mansy SS et al. Template-directed synthesis o...[PMID: 18528332]


Mansy SS et al. Reconstructing the Emergence ...[PMID: 19734203]


Martin W et al. Hydrothermal vents and the or...[PMID: 18820700]


The Origin of Life


How life evolved: 10 steps to the first cells


Was our oldest ancestor a proton-powered rock?




7.  Synthetic cells have nearly been synthesised.


Murtas G. Artificial assembly of a mini...[PMID: 19823743]


Schwille P et al. Synthetic biology of minimal ...[PMID: 19635039]


Loakes D et al. Darwinian chemistry: towards ...[PMID: 19562107]


Solé RV et al. Synthetic protocell biology: ...[PMID: 17472932]





Intelligent design (ID) debunked


Complex-specified information (CSI)


         Intelligent design (ID) is the idea that certain features of the universe and living things are best explained by an intelligent cause such as an intelligent agent.


Primer: Intelligent Design Theory in a Nutshell


It is based on the idea of complex-specified information (CSI), which is usually based on Dembski’s filter. Irreducible complexity is a subset of CSI saying that certain biological systems are too complex to have evolved from simpler, or “less complete” predecessors because all of its parts must initially be present in a suitably functioning manner.


The Amazing Cell


Dembski’s filter is basically:


Does event E have a high probability or can it be explained by a law? If no:

Can it be explained by chance? If no:

Having rejected regularity and chance, must accept design.


More specifically, Dembski arbitrarily defines CSI as nonrandom information with 500 bits or more.


         Basically this is wrong because natural selection can produce information. Dembski assumed that natural processes are incapable of producing information exceeding 500 bits. This is not so. The very early genomes were very small and contained no information. It was due to the natural selection for efficient replicators that information increased. Evolutionary mechanisms also increase information and have been operating on cells for BILLIONS of years. The filter ignores all this.


         Another problem is that the first step asks for probabilities that are unknown, so we simply cannot perform the calculation. Also, success is badly defined and focuses on a single, specified outcome. For example, many different protein sequences can give a particular function, not just one. So it is wrong to calculate the probability of just one particular sequence.


Creationism special: A sceptic's guide to intelligent design



Irreducible complexity


         Behe’s irreducible complexity is also simply wrong. The systems that Behe cites have all been proved to have been able to have evolved naturally:


The “bacterial flagellum”


Pallen MJ et al. From The Origin of Species to...[PMID: 16953248]


This paper shows that

a) There are many different forms of the bacterial flagellum, varying in structure and mode of function and that in fact most consist of a conserved core of only about 30 proteins. This only about half of the flagellum proteins in some species, suggesting the system in these species is not even irreducibly complex.

b) Vestigial non-functional remnants of flagellar genes have been found in several bacteria.

c) Flagellar proteins have homology with each other, suggesting common evolutionary ancestry.

d) They also have homology to other non-flagellum components, further suggesting evolutionary origins.


Snyder LA et al. Bacterial flagellar diversity...[PMID: 19081724]


This paper shows that

a) Cut-down flagellar systems have other roles besides the flagellum.

b) Many of the proteins have functional homologs in the geneomes.

c) Not all bacteria have flagellums and that the taxonimical distribution of the genes could be a gene loss or horizontal gene transfer (HGT) scenario.



The eye


Fernald RD. Casting a genetic light on th...[PMID: 17008522]


This shows the evolutionary “stepping stones” for the formation of eyes.


Trezise AE et al. Opsins: evolution in waiting....[PMID: 16213808]


Shows the evolution of the proteins that allow us to see – opsins.





         There are also examples of complicated protein complexes that have had their evolutionary history resolved. An example is complex 1:


Gabaldón T et al. Tracing the evolution of a la...[PMID: 15843018]



There are many examples like this, which show macromolecular complexes had plausible evolutionary “stepping stones”.


         Other ID proponents like Meyer make the same mistake of viewing DNA just like a code completely ignoring its evolutionary history, therefore fallaciously concluding information arose without a naturalistic explanation.


Jefferson would not have supported intelligent design




According to a literal interpretation of the Bible, God is evil.


Leviticus 25

God says it’s okay to have slaves from other nations.

Genesis 3

God punishes ALL women with the pain of childbirth and subjugation to man just because of the sin of just 2 people.

Genesis 11

God intentionally confounds the languages of men to impair their communication.

Genesis 7

God murders the whole of humanity and kills all animals on earth except for Noah and co.

Exodus 11

God murders hundreds of children (first born).

Exodus 32

God punishes people for making a golden calf.

Judges 3:26-37

God helps Ehud kill lots of Moabites.

1 Kings 20:30

God kills Syrians by causing a wall to fall on them.

Ezekiel 9:6-7

God orders the killing of women and little children without pity.

1 Samuel 15

Samuel hewes Agag into pieces in front of God.

1 Samuel 15:1-3

God instructs the murder of women and children and animals.

Leviticus 24:10-17

God instructs the public stoning of a man who blasphemed.

2 Chronicles 21:12-16

God intentionally gives a person bowel disease.

Judges 16:26-33

God inspires Samson to kill men and women who weren’t attacking him.

2 Kings 2:23-25

God sends bears to rip up children for calling Elisha bald.




Literal interpretations of some passages of the Qur’an and the Hadith can motivate fundamentalist behaviour


Hadith (Sahih Bukhari), Volume 9, Book 84, Number 57

... 'Whoever changed his Islamic religion, then kill him.'


Qur'an 9:123

O ye who believe! Fight those of the disbelievers who are near to you, and let them find harshness in you, and know that Allah is with those who keep their duty (unto Him).


Qur'an 9:5

Then, when the sacred months have passed, slay the idolaters wherever ye find them, and take them (captive), and besiege them, and prepare for them each ambush.


Qur'an 9:29

Fight those who believe not in Allah nor the Last Day, nor hold that forbidden which hath been forbidden by Allah and His Messenger, nor acknowledge the religion of Truth, (even if they are) of the People of the Book, until they pay the Jizya with willing submission, and feel themselves subdued.


Qur'an 24:2

The woman and the man guilty of adultery or fornication,- flog each of them with a hundred stripes: Let not compassion move you in their case, in a matter prescribed by Allah, if ye believe in Allah and the Last Day: and let a party of the Believers witness their punishment.


Qur'an 4:34

Men are the protectors and maintainers of women, because Allah has given the one more (strength) than the other, and because they support them from their means. Therefore the righteous women are devoutly obedient, and guard in (the husband's) absence what Allah would have them guard. As to those women on whose part ye fear disloyalty and ill-conduct, admonish them (first), (Next), refuse to share their beds, (And last) beat them (lightly); but if they return to obedience, seek not against them Means (of annoyance): For Allah is Most High, great (above you all).



The Center for Muslim-Jewish Engagement, Quran




The Bible is scientifically incorrect.


Genesis 1

  1. The formation of the universe is inaccurately described.
  2. The Earth was formed after the sun, not the other way around.
  3. Stars are described as “lights in the firmament of the heavens”. That is incorrect.
  4. The origin of animals and humans is incorrect.
  5. The timescale of the formation of the universe is incorrect.
  6. The origin of sexual dimorphism is incorrect.

Genesis 5

  1. The longevity of early humans described is impossible.

Genesis 7

  1. The global deluge described is impossible because it wouldn’t have left the geological layering pattern we observe, namely clearly defined sedimentary layers each made of different material and in no particular order.

Genesis 8

  1. The repopulation of the Earth’s human and animal population on the ark is impossible because it doesn’t coincide with the patterns of genetic markers we see today.


         There are many other scientific falsehoods that have been omitted. Many of these are available here:


The Skeptic's Annotated Bible




Destructive impact of Abrahamic religions


         The religious claims of Abrahamic religions are often destructive belief systems. Here is a partial list if the wars, conflicts and detrimental effects that they inspired.


  1. The Crusades
  1. Northern Ireland conflict
  1. The Spanish inquisition.
  1. The Israeli-Palestine conflict
  1. Indo-Pakistani war
  1. Domestic discrimination of religious minorities throughout history solely because of their religious beliefs. This includes the burning of innocent women as witches.
  1. Christian theocracy was widespread in the Dark Ages, one of the most brutal periods of history. It also marked 1000 years of scientific non-achievement.
  1. Several historians and scientists speculate that Islamic fundamentalism contributed to the scientific decline in the Islamic world by failure of separation of science and politics and that modern science was antagonistic to the metaphysical presuppositions of Islam.
  1. Various acts of violence throughout the world, including terrorist attacks, can only be explained by motivations from Abrahamic religions.




Atheism is a more healthy belief system than Abrahamic religion.


1.  Atheism correlates positively with IQ

R. Lynn, J. Harvey, and H. Nyborg. Average intelligence predicts atheism rates across 137 nations. Intelligence, 37(1):11–15, January 2009.


2.  Only about 7 % of leading scientists in the US believe in God. This probably even lower in Europe.

Leading scientists still reject God, Nature, Vol. 394, No. 6691, p. 313 (1998)


3.  Atheist countries do better in indicators of social welfare.

Gregory S. Paul. Cross-national correlations of quantifiable societal health with popular religiosity and secularism in the prosperous democracies. Journal of Religion and Society, 7, 2005.


The Times, September 27, 2005, Societies worse off 'when they have God on their side'


Eurobarometer Special Surveys

See section 1.2. Religious and spiritual beliefs.


4.  Atheists have a higher education level in the USA.

American Beliefs: Evolution vs. Bible's Explanation of Human Origins


5.  In the USA, church attendance by state positively correlates with property crime (Burglary, Larceny-theft, Motor vehicle theft) significantly.

Church Attendance Lowest in New England, Highest in South


Crime in the United States


linear model:

r= 0.369465459107821

p= 0.008984274775932





General links to primers and resources


         These are some short primers and resources that review some basics of the science behind cosmology and evolution. They can serve as general introductions.


Physics and cosmology




Why it's not as simple as God vs the multiverse


Hints of 'time before Big Bang'


Science's Alternative to an Intelligent Creator: the Multiverse Theory


Multiplying universes: How many is the multiverse?


Mitton S. Astroparticle physics and cos...[PMID: 16714191]


Steinhardt PJ et al. A cyclic model of the univers...[PMID: 11976408]





Parallel Universes, BBC


Steven Weinberg Discussion (1/8) - Richard Dawkins








Understanding Evolution


Pagel M. Natural selection 150 years o...[PMID: 19212397]


Evolution on the Front Line




Evolution: 24 myths and misconceptions


Evolution on the Front Line





Tree of Life video HD


Evidence for Evolution, Part I


Evidence for Evolution, Part II


How Evolution Works- Introduction (Part I)


Evolution IS a Blind Watchmaker


Debunking "creation science"