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)*...(0.5)^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.

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.

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.

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. 

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]  

Clay

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. 

Nutfah

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.

Alqahah

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.

Bones

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. 

Conclusion

 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.

It's not a sinful life

Atheists often get told they've become so for irrational reasons.  One of the most fatuous claims I've heard (and I'm sure I'm not unique), is that I've become an atheist because I love to sin.  In short, I really know there is a god, but I'm just pretending there isn't because I prefer some kind of sinful life.

This betrays almost no prior thought.  If anyone really believed there was a supreme deity with the attributes ascribed to it (love, unconditional mercy etc) then there isn't really any motive to pretend otherwise.  Especially when you'd be willingly choosing an eternity of presumably, heinous torture (as many theists are fond of reminding me).  Does this actually make sense as an argument?  I know there's really a god but I prefer infinite torture to some kind of eternal paradise?  It's got to be one of the dumbest arguments I ever hear.

Especially, as I should point out, that if you are a theist, you're not banned from sinning.  If you're a theist, you can sin (you have to, it is in your nature because of original sin or some other imperfection). And you still avoid hell.  So you get it all.  Atheists are smart enough to figure that out.  There's no reason to pretend.  We genuinely have no belief in the gods that have been supplied to us.

For the most part, people become atheist for a very mundane reasons.  There is no credible for gods, and the whole concept often sounds wildly implausible.

Prayer Fails

The widespread belief amongst the faithful that intercessory prayers are effective at curing disease is strong.  It is sufficiently strong that it doesn’t waver when children like the Schaibles die of medical neglect. The faithful watch children die as their bronze-age chants fail, and feel no remorse, no doubt.

The best scientific study working with large groups on the effectiveness of prayer remains with Benson et al (2006) [1]. The study overcame the methodological weakness of previous studies by using proper randomisation of subjects and ‘blind’ techniques, combined with large sample sizes.

About 1800 coronary artery bypass graft (CABG) patients were in the study. The patients were randomized, such that only 1/3 knew definitely they would receive intercessory prayer to assist recovery. The other 2/3rd did not know if they would receive prayer. Half of them did, half didn’t.

The study showed that prayer had no effect on complication-free recovery from CABG. The group that did know they were receiving prayer however, had a significantly higher risk of complications (59% versus 51%). It was speculated that knowing they were receiving prayer, increased their anxiety (perhaps they were sicker than they had been led to believe) and this contributed to the increased rates of complications.

There is no scientific evidence that validates the belief that prayer is effective at curing disease.
—
[1] Herbert Benson MD, Jeffery A. Dusek , Jane B. Sherwood , Peter Lam , Charles F. Bethea , William Carpenter , Sidney Levitsky , Peter C. Hill , Donald W. Clem, Jr. , Manoj K. Jain , , David Drumel , Stephen L. Kopecky , Paul S. Mueller , Dean Marek, Sue Rollins ,  and Patricia L. Hibberd (2006). Study of the Therapeutic Effects of Intercessory Prayer (STEP) in cardiac bypass patients: a multicenter randomized trial of uncertainty and certainty of receiving intercessory prayer. American Heart Journal 151(4): 934-942