Saturday, 14 January 2017

Fumbling Apologetics

Is it possible to be an honest apologist?

Recently on twitter an apologist (S J Thomason) has been arguing with atheists.  An odd tactic is to post a blog (see link), claim it defends Christianity, then claim victory on dissenters on twitter.  As it's difficult to deal with this within 140 characters, I'm posting a response to one of her arguments here.  It is on the topic of evolution, which I can at least claim to be familiar with.

SJ Thomason writes:

Atheist challenge: Christians don’t believe in evolution, which is proven by science.

 This is false and disappointingly dishonest. Atheists don't claim that.  Many Christians accept that evolution occurs.  Many of the scientists who have contributed to the theory are Christian. Dobzhansky for instance, was one of the founders of the modern synthesis, provided the first gene-based definition of evolution, and was Christian.  The problem occurs when evolution conflicts with the doctrinal beliefs of some Christians.  Thus some Christians won't accept that species are mutable, or that humans evolved from a species that was the common ancestor to all other ape species. .

Christian rebuttal: Many theists support the idea of evolution, yet we must distinguish precisely what “evolution” means. We have witnessed and have archeological data indicating the evolution of humans, yet we don’t have any data bridging the gap between the primordial soup that ignited life on this planet and the earliest forms of life that contained consciousness.

 Evolution means a change in the allele frequency (heritable) traits in populations over generations.  This can manifest as both the increases in antibiotic resistance in bacteria up to the changes that caused a small terrestrial artiodactyl to become a whale. 

We have plenty of data linking the earliest life-forms to extant amniotes like us.  All cellular life shares a basic tool-kit of genes, it uses the same genetic code, cell walls are bilayer lipids, we all use ATP as the currency of energy.  Many molecular phylogenies show convergence to a single, universal ancestor. Not multiple ancestors that arose at different times. A single one. To claim we don't have any data linking us to the earliest life is brazenly ignorant and dishonest.

The evolution of the unconscious to the conscious is unexplained by science, suggesting the presence of a guiding force – an intelligent design.(11)

There are many things we have yet to explain in biology.  That's not evidence of an intelligent designer, or specifically a Judaean bloodgod with a penchant for mating with virgins.  Intelligent design has produced no research, nor even proposed testable hypotheses on consciousness.  There is nothing rational about inventing a deity to explain what you don't understand.

Given consciousness does seem affected by biochemical pathways, and emerges gradually as embryos develop, your alternative explanation is neither evidenced nor reasonable.

“Because of the way earth was and now is, it affords habitats for three radically different kinds, or categories, of life: (1) physical; (2) physical and mind-possessing; and (3) physical, mind-possessing, and spiritual.”(12)

 These arbitrary categories aren't statements of fact, but religious claims. Humans, birds, plants and fungi are not radically different kinds of life.  They occupy the same domain. A spiritual dimension cannot be invoked without evidence.

Until atheists can bridge the gap between the physical and the physical, mind-possessing and spiritual, Christians will disclaim the form of evolution that they propose, which is the form that claims that everything evolved from a pond of primordial soup.

 Molecular evidence already provides strong support that all life is related to a common ancestor (LUCA).  That it conflicts with your religious beliefs isn't a valid rebuttal of the evidence.  Please note that the phrase 'primordial soup' is eschewed by most researchers who work on the origin of life.  It is rather, a creationist shibboleth

Monday, 5 December 2016

10 Reasons why I'm not a Christian

Internet Christians seem fond of the "list approach" to proselytizing.  This comes in various forms. Like "10 reasons Christianity is true" or "10 questions atheists can't answer".  So with that inspiration, here are 10 objections I have to the existence of the Bronze-age Deity Yaweh and his magic carpenter son.

1. The absence of evidence where there should be evidence

Depending on your flavour of Christianity, this particular deity is supposed to have created the Universe, formed the earth, begun life, created humanity from just two individuals, intervened frequently in the affairs of a Near Eastern Tribe, and made a personal appearance for approximately 33 years.  Many of these events should leave compelling evidence. Genetics should confirm we descended from just two individuals. Other civilizations should have noticed the extraordinary events described in the bible.  That evidence is just not present.
Genetics confirms that modern human species never originated from just 2 individuals

2. The Soap Test

There are no instructions on using soap.  Soap is a product that is easy to make.  It also has benefits for hygiene as well as reducing infections and limiting the spread of disease.  These effects on disease were not realised until the 19th C when Ignaz Semmelweis used it in hospitals to reduce patient mortality.

Any deity that is supposed to be benevolent, all-knowing, and interceding to benefit a chosen tribe or people, would give instructions on its use.  Instructions on its use however are weirdly absent.  This neglect would have increased needless suffering (through illness and disease) as well as premature deaths. With no technological barrier to making soap, there is no valid reason to withhold instructions on its use. Given the vast number of people whose lives would have been improved by providing instructions, it's not a trivial issue.

3. The gospels are problematic

Not only are the gospels written well after the alleged events, they contradict each other in key details.  The nativity of Luke and Mark describe entirely different events.  Unlike Julius Caesar there are no writings of Jesus. No contemporaneous historian, of which there were several in this era, noticed any of the fantastic things described in the gospels.

One feels an omniscient (all-knowing) deity would know this would reduce the confidence non-believers would have in the Jesus-mission. Even Julius Caesar left stuff he wrote. And an all-powerful deity might have ensured the records of the Jesus-mission weren't so dependent on the contradictory, hearsay accounts we have.

4. Prayer doesn't work

Enough children have died in faith-healing cases to show that prayer only succeeds in mundane cases with a high likelihood of occurring anyway. There is no evidence at the population-level that Christians are healthier, live longer or recover from cancer more frequently.

5. How about those slaves then?

Right, Christianity has always been against slavery. Even in the first 1800 years when it wasn't.  And as the American Civil War showed, for many, not until the Federal Army reached Richmond.  The problem is that Jesus never said to abolish slavery. Neither did anyone else in the bible. Indeed, Exodus 21:20-21 said it was permissible to beat a slave so badly that they would die 2-3 days later.  The slave-owner wasn't punished in this case as the slave was his property. A chattel. Not a human being, but property.
Black Slaves (Wikipedia Commons)

This is a very simple test. Moral beings don't sanction this horrific behaviour.  Christianity perpetuated slavery. It's failed to reach a credible standard of morality that would corroborate a loving, moral supreme deity.

6. A peculiar dislike of poor black people

One appreciates that life on this planet is a little chaotic.  That means natural disasters happen.  I'm not quite sure how a loving deity allows people to die in natural disasters, as the freewill argument seems moot in these cases.  The deaths and suffering are not caused by human agency.

Tent City- Port au Prince (Wikipedia commons)

Nonetheless, the real point is how unjust these disasters are.  They impact the poorest and most vulnerable communities the most.  In 2010 a magnitude 7.0 earthquake hit Haiti.  The death toll was somewhere between 100,000-300,000 people. The same year a 7.1 earthquake hit Christchurch in NZ.  One person died of a heart-attack, that might have been caused by it.  The effects are not equal.

If we're going to propose any kind of argument that humans have to put up with natural disasters, at the very least, these should not be so manifestly unjust.   Having a system that harms those communities least able to cope contradicts the alleged characters of the Christian deity.

7. Baby I call Hell

Like everything to do with the afterlife, Hell is difficult to pin down.  Is it a place of heinous torture as described by Dante and other evangelical pastors?  Or is is an eternal separation from this deity?  Given the wide-spread dogmatic belief that it is torture (and I've been threatened often enough with it), then it's irreconcilable with a just and loving deity.

 The infraction against this god is transitory in nature. All I have done is not believe it existed. That merits an infinite punishment- one that is unusually cruel, barbaric and inhumane.

Hell- Wikipedia Commons

Hell and a loving, just deity cannot both exist.

8. She blinded me with science

I appreciate that ancient people could not have had with their knowledge, the language of concepts to describe the world in scientific terms.  Nonetheless, it seems odd that many ideas about the world are simply and blatantly wrong.  The microscopic world, the scale of the universe, that earth is not its centre, that life originated billions of years ago and then evolved are in conflict with many religious dogmas.  It's not a good advertisement for these beliefs to be true.

9. It's a small world

It is inescapable that the events of the bible are restricted to a tiny part of the world.  Most of Asia, Africa, the Americas and Oceania are excluded.  For a universal deity, this is suspiciously parochial.  It is according to the Abrahamic religion capable of communicating in all kinds of ways.  There are burning bushes, talking donkeys, angels etc.  But only a small tribe of pastoralists are selected for this direct communication.  In particular, a tribe that whose accomplishments were so minor, they had little ability to communicate their god to others.  While civilisations around them developed maths, astronomy, engineering, democracy and philosophy, ancient Judea developed, well, penis modification.

Even within that context, only a small part of the population is considered worthy of this message.  This part being men, of course.  For a universal deity that considered all to be equal, this incredible favoritism does not make any sense.

10. Free Fallin'

The problem with an all-knowing (omniscient) god is well known.  It makes free-will a fantasy.  If a deity knows everything I'm going to do and say over my life-time, there's nothing I can do to change that.  If Abe's god knows I'm going to have sushi for lunch, then I cannot choose anything else.  That extrapolates to every other action I take, to very word I utter.  I cannot choose anything, choice is an always following a single course of action.  I can only say the lines I was given.  I can only play the role I was destined to play.

Life in this case, is meaningless.  If I am going to hell, then, nothing I do over my life will change that.  I can only undertake the actions this deity already knows I'll take.  All life is, is a brief moment where I can change nothing, followed by an eternity of hell.  There's no point to this life at all.  This god may as well put those destined to hell, straight there.  Because nothing will change that destiny.

Monday, 6 June 2016

How improbable is it that proteins can form by "chance"?

A common trait of scientists who work on the origins of life, is not to attempt to estimate the probability macromolecules (like peptide chains) will form. A common trait of creationists who don't, is estimating such probabilities.  This typically produces astronomical odds against such macromolecules forming.

For instance, suppose we are told there is a 50:50 chance that two amino acids will bond.  A peptide-chain (protein) 150 amino-acids long, will thus have the probability of (0.5)*(0.5)^2*(0.5^3)*...(0.6)^150.  This gives a cumulative probability of well, a really really big number against (1 in 1045 IIRC).  Thus the number of trials needed to make this peptide seem up there in many billions of trillions.

The problem above is simple. It ignores the fact that macro-molecules form in a modular fashion. (There's also some assumptions about the chemistry also, but we'll put those aside).  Macromolecules don't form one molecule at a time, in one go.  If we just add one correction to the calculation above- that the peptide chains form in a modular way, it takes just 5 trials to make a chain 150 amino-acids long.  That's right. Just 5.  The Creationist result above are entirely produced by unrealistic assumptions.

Let me demonstrate.  We start with a large pool of amino-acids.  There's a 50:50 chance in the first round, they bond to another amino acids (using SIPF chemistry, dipeptides are found within a week).  This is merely the assumption from the creationist maths above.

So after trial 1:
Half the amino-acids have formed dipeptides (a chain of 2 amino acids)

Half the amino acids are still unpaired to anything.

We then carry these into trial 2:
Some of the amino acids will still not have bonded.  Some will form dipeptides.
Some of the dipeptides will bond to one other single amino acids (making a tripeptide)
Some of them will bond to another bipeptide, or to two single amino acids.  (Bonding can occur at either end of the chain, it doesn't have to be at just one end).  That's an oligopeptide 4 amino-acids long.
Importantly, some of the dipeptides will bond to two other dipeptides.  After two trials, we will find peptide chains 6 amino-acids long.

On to trial 3:
Some of the peptide chains 6 amino-acids long, will bond to two other 6 amino-acid peptides.  Some of the peptide chains are now 18 amino-acids long.  The distribution of peptide chains in the pool will range from 1 to 18 amino-acids long.

On to trial 4:
Some of the 18 amino-acid chains will bond to two other 18 amino acids.  We will find in the sample, anything between 1 amino acid to chains 54 amino-acids long.  

On to trail 5:
If 3 peptide chains that are 50-54 amino-acids long bond, then we've got our 150 amino-acid peptide chain.  We didn't need trillions of trials. It's that simple.

Ok.  This is a gross simplification.  The chemistry of peptide formation is a lot more complex than just two molecules randomly bonding.  That's why people who actually work in this topic, don't try to calculate probabilities.  There are too many variables and too many permutations to make any estimate meaningful.  The point is to show how utterly devious and dishonest it is, to drop the modular assumption of macro-molecule formation.  And why you actually need to use a Markov probability function, not an IID.  What happens in each trial is not independent of previous trials. The reason creationists use an IID is because it's the one function everyone knows, and it wildly inflates the improbability of anything happening.

Wednesday, 7 October 2015

The Dilemma with "Kinds"

@Atheistic_1 Sep 27 (Twitter)

Kent Hovind breaks down "kinds": "Everyone knows birds are different than fish." 

Anyone familiar with creationists know that they generally eschew scientific classification of organisms. Rather, they try to reclassify life into what is they term kinds.  It doesn't take long to work out they can't actually define kinds.  They'll throw out what they think are examples of kinds, but they cannot specify the criteria to separate kinds.

So why not simply treat kinds as a synonym for species?  The answer is the Ark.  The idea that all of this planet's terrestrial animal species could fit on the Ark (and let's face it, this is supposed to include extinct taxa like dinosaurs also), is impossible.  So by using larger groups, the cramming task is made less difficult.  Perhaps there is only one cat-kind. Thus all Noah needed was this single pair, rather than representatives of all extant Felidae.

Kinds need a broad definition to fit everything into the Ark

So kinds have to be defined in a broad way, to cluster lots of species together.

But kinds have to be narrowly defined to separate us from apes
This creates the dilemma. The dilemma is us- humans.  Genetically we are more closely related to chimpanzees, than chimpanzees are to gorillas (and other great apes).  So if the point of using kinds is to 'cluster' animal species into groups, we'd be a kind of chimpanzee (or even an ape).  This conflicts with a special creation of humans out of dirt.  We are according to creationists, distinct from all the other animals. This means kinds has to be now revised to mean something incredibly narrow.  It has to be so narrow it can separate us from all other ape species.

The requirement for kinds to be both a way of broadly defining life, and at the same time, even narrower than scientific classification systems, is impossible to pull off.  And for that reason, kinds cannot ever be supplied with an actual definition.  They can only flounder in their futile attempt to meet their two goals.

Monday, 17 August 2015

The problem with witches

There are many reasons I don't believe in the god of Abraham. One of these reasons is the killing of "witches". This brutal fact, this product of religion,  is completely at odds with the alleged traits of this god.  In short, if there is an omniscient being (who knows all) and who truly cares for humanity, then the hideous deaths of those accused of witchcraft refutes that entity.  Let me elaborate.

The bible is very clear on what to do with witches.
Thou shalt not suffer a witch to live Exodus 22:18
Because witchcraft is a fictional crime, it means throughout history, countless innocents have died as a consequence of this.  Some 40-50,000 people have been killed for witchcraft in Western countries, many in quite hideous ways.  Violent attacks on witches still continue today. A UNICEF 2010 report details attacks on child-witches sic in Africa. Children with disabilities are especially targeted. Such attacks are far more common in Christian communities than Muslim.  The link is to the biblical command to kill witches. 

Now clearly, an omniscient entity would know all of this back in the "Exodus" era.  It would know that including this command would mean say, that a child with epilepsy, would be betrayed and violently attacked by the adults in his or her community. That even if they did not die, the risks they faced would inflate the likelihood of an early death.  About 20,000 streetchildren had been accused of witchcraft in the DR Congo capital Kinshasa

Knowing this, knowing that mere children would be murdered as a consequence of Exodus 22:18, this entity still allows it to be included.  So here's the question. If you knew that this edict would result in the deaths of thousands of innocents, that children would be attacked and murdered, would you include it in a text that communicated your wishes? 

This is the dilemma. If you include it, you will be responsible for the inhumane deaths of these people. If you were a benevolent and loving and deity- and your omniscience meant you could see the consequences of all your edicts- would you really include this passage?

Let's play the context game. Let's play the excuse that this is all Old Testament stuff. That there is some context here that's been overlooked. Overlooked for centuries even, as killing people for witchcraft as been a Christian tenet for most of its history.

So, as an omnipotent and benevolent being, you have the means to tell the faithful that this verse say, no longer applies (or is being applied incorrectly). You can appear as a burning bush, or a talking donkey. You can send angels as messengers. If Christianity is correct, you can even make a physical manifestation of yourself as your own, mortal son about 2000 years ago.

So about 2000 years ago, all you had to do was say something. Not do something, not change the laws of the universe. All you'd have to do is explain that Exodus 22:18 no longer applied.

If you did that, then thousands would not have died in flames in Europe.  Kids with epilepsy or autism would not be beaten, assaulted or killed.

Such a little thing.

Yet there is no record of this.

I doubt that anyone of us, with so many lives at stake, with the most vulnerable people (kids with disabilities) being the target of this, could choose not to make this clear.

You cannot claim there is an omniscient, moral and benevolent, who intercedes in this world, when the body-count of the innocents is so high. Omniscience means you must know what Exodus 22:18 leads to. Benevolence means you must do everything to prevent the consequences of that. Omnipotence gives you the power to do so. In no state of the world, does this combination explain why kids are being killed for witchcraft.

Friday, 20 February 2015

Scientific Definitions of Evolution

The "Modern Synthesis", which is the foundation of modern biology, occurred during the 1930s and 1940s.  It brought together Darwin's evolutionary mechanisms of selection (noting Darwin explicitly stated these were not the only mechanism), with Mendelian genetics and paleontology.  Combining Mendelian genetics with Darwin's mechanisms took the work of Fisher and the like.  These used statistical methods to show how gradual changes would occur.  Paleontology  by this stage, had discovered sufficient transitional forms to make evolution on these geological time scales accepted.

This synthesis provides the definition of evolution we use today.  The term 'descent with modification' is more a description than a definition.  I list a sample of these definitions here.  The key points is that evolution is about genetic, inheritable changes in populations.

Non-inheritable changes (like amputations) are not evolution.  Evolution does not mean a cat gives birth to a dog, or a monkey gives birth to a human.  It operates at the level of populations.

Theodosius Dobzhansky (1937) Genetics and Origin of Species
Evolution is a change in gene frequencies through time
John Maynard Smith (1958) The Theory of Evolution
 Evolution is merely a reflection of changed sequences of bases in nucleic acid molecules
David L Kirk (1980) Biology Today. 3rd ed.
a progressive, heritable change in gene frequencies in a population through succeeding generations, as a consequence of processes such as mutation, natural selection, and genetic drift
 Helena Curtis and N. Sue Barnes (1989), Biology, 5th ed.
In fact, evolution can be precisely defined as any change in the frequency of alleles within a gene pool from one generation to the next. 

Sunday, 4 January 2015

Embryology and the Qur'an

The internet provides a vehicle for many to communicate their beliefs.  Muslims have also taken to social media (like twitter) to proselytize for their religion. A popular tactic is to claim that the qur'an is filled with modern scientific knowledge.  This seems to be a bizarre tactic.  The Islamic world has not really been at the forefront of scientific discovery since, well, Copernicus worked out that the solar system was heliocentric before Muslim astronomers.  Despite studying an ancient book that provides apparently, all kinds of useful pointers on modern science, the Islamic world is deeply under-represented in science Nobel prizes etc.

One of the claims does interest me as a biologist, and also as an atheist who gets this ploy used on me a lot.  This is the claim that the qur'an anticipates modern (human) embryology.  This could only have a divine origin (despite its erstwhile similarities to Galen, for whom no such divine inspiration is attributed).
Human Embryo

The relevant verses are 23:12-14.  So I just want to look at these quickly.
We created man from an extract of clay. Then We made him as a drop in a place of settlement, firmly fixed. Then We made the drop into an alaqah (leech, suspended thing, and blood clot), then We made the alaqah into a mudghah (chewed-like substance)...
[Noble Quran 23:12-14]  


23:12 claims that humans are made from clay.   Now because clay is mostly aluminum and silicon and contain little of the organic material this is clearly not the case (the 6 macro-elements we look for as life's basic building blocks are Hydrogen, Oxygen, Nitrogen, Phosphorus, Carbon and Sulphur). It is perhaps more likely this is meant in an allegorical rather than scientific sense.  But if we accept this is not being scientific, then well, it is not clear why the remaining verses are supposed to be scientific. 


23:13 introduces the drop (nutfah) which also presents problems. It doesn't take divine inspiration to realise that the ejaculate from a male can be a liquid drop.  It would be impressive if the qur'an mentioned sperm and eggs.  But it doesn't. In fact, eggs (baydeh) are nowhere mentioned.  It strikes me that as a guide to modern embryology, omitting any mention of eggs is well, astonishing. Parenthetically, sperm isn't mentioned either. Sometimes special pleading is used to infer that the nutfah means a human gamete. But there is nothing here that hints at the microscopic world. 

The claim of a safe lodging would also contradict ectopic pregnancies, where the gamete might settle in the fallopian tube or abdomen. This unsafe location causes miscarriages or at worst, painful pregnancies fatal to mother and child.


23:14 then gets very complicated as many words gets vaguer. The first stages of  embryology (blastula, gastrula) don't involve any blood vessels, so a clot isn't a good description.  It seems more plausible that the spotting that sometimes occurs in early pregnancies- or even miscarriages- would cause a 'blood clot' deduction.  

Alternatively, alaqah could be a metaphor based on a leech.  If so, it is not a very good one.  Leeches are protostomes whilst humans are deuterostomes. We haven't been alike for about 600my. Leeches lack a notochord, they lack limb buds, they lack pharyngeal arches.  A human embryo doesn't digest its host's blood. It doesn't use its mouth-parts to interact with its host.  

Even if we want to go with a leech-like interpretation over the blood-clot for alaqah, then this does not imply divine insight.  For a people familiar with butchering animals (and dare I say, people on occasion), it wouldn't take much powers of observation to notice small embryos attached to the uterus of pregnant mammals.  For ancient peoples, these likely resembled leeches.


The text above omits the last part of 23:14.  Here are two translations of it:

Muhsin Khan Then We made the Nutfah into a clot (a piece of thick coagulated blood), then We made the clot into a little lump of flesh, then We made out of that little lump of flesh bones, then We clothed the bones with flesh, and then We brought it forth as another creation. So blessed be Allah, the Best of creators.

Pickthall Then fashioned We the drop a clot, then fashioned We the clot a little lump, then fashioned We the little lump bones, then clothed the bones with flesh, and then produced it as another creation. So blessed be Allah, the Best of creators!
The issue here is simply the order bones appear. It appears to describe two stages. First, the mudghah becomes bones, then the bones are covered in flesh. This is likely a deduction of people used to butchering animals, and had no way of conceiving how muscles and flesh could be attached to bones without the skeleton being formed first.

The problem is that bones form last. Reduced to the basic steps, mesenchymal cells within the embryo first differentiate into cartilage lines. Later this cartilage is replaced by bone. At no point would we say that the bones are later covered in flesh. 


 It is obvious that the qur'an does not describe human embryology at any useful level.  Rather the argument depends on some very heroic special pleading. Modern scientific discoveries are retrofitted to vague language to make claims that go far beyond the verses.  It also depends on poor knowledge of embryology.  No quantity of Youtube videos or webpages can hide the fact that the Qur'an simply does not describe human embryology.  Rather than being special advanced knowledge, the qur'an seems entirely consistent with knowledge of the era. I'm reluctant to believe that the "creator of the universe" sic would know as little biology as the typical 6th C Arab.