Monday, 25 February 2013

Abusing Thermodynamics: Duane Gish

The Institute for Creation Research has an article by Duane Gish with some abuse of thermodynamics:
http://www.icr.org/article/177/

The article says: "The Second Law of Thermodynamics states that matter and energy always tend to change from complex and ordered states to disordered states." No. Overall entropy increases, but in one place it may well decrease. A simple example would be a hot cup of coffee. As it cools its entropy decreases. The second law is not being broken; as the cup cools heat is lost to its surroundings and overall entropy increases.

Further, the Second Law has nothing about complexity - it is only about entropy, which is disorder of energy. This is a common addition that creationists like to slip in.

They make it clear that this guy has a Ph.D., so he should know what he is talking about. He has a degree in chemistry and a Ph.D. in biochemistry, both from decent universities, so it is seems a good bet he knows and understands thermodynamics. When he is peddling this nonsense, well, it looks like the guy is just lying.

With regards to the universe, Gish says: "... it would have run down long ago." How did he calculate that? An assertion counts for nothing. This really is the totality of his Second Law argument against the Big Bang.

With regards to life, he goes on to say:
The Second Law of Thermodynamics states that things tend to go from order to disorder (entropy tends to increase) unless added energy is directed by a conversion mechanism (such as photosynthesis), whether a system is open or closed. Thus simple molecules and complex protein, DNA, and RNA molecules seemingly could not have evolved spontaneously and naturalistically into a living cell;4 such cells apparently were created.
Again, we see this confusion about what the Second Law says. Overall entropy goes up, but that does not prevent entropy decreasing locally. Trees grow, cups of coffee cool, snow flakes form. There is no problem with entropy going down in one place, as long as it increases overall.

To head this off, he says "unless added energy is directed by a conversion mechanism", but this is just something he has made up. Look at the mathematical relationship defining the Second Law:

S(i) < S(f)

... where S(i) is the intial energy, S(f) is the final energy.

Where does it something about mechanisms? Where does it allow for an "unless"? There is no "unless" in the Second Law; it is universal. Look at the cooling cup of coffee and tell me where the "conversion mechanism" is!

And a guy with a degree in chemistry should know that.

Friday, 22 February 2013

Abusing Thermodynamics: Charles B. Thaxton

A great example of abusing thermodynamics can be seen in the book The Mystery of Life's Origin, by Charles B. Thaxton, Walter L. Bradley and Roger L. Olsen. Chapter 8 is available on-line here.

This chapter was written by Thaxton, who has a Ph.D. in physical chemistry, so really should know better. He considers the entropy when polypeptides form. A polypeptide is a sequence of amino acids, and he compares a random sequence with five each of the twenty biologically active amino acids to a specific sequence:
For a random polypeptide of 100 amino acids, the configurational entropy, Scr, may be calculated using eq. 8-2c and eq. 8-7 as follows:

Scr = k lncr

since cr = N! / n1!n2!...n20! = 100! / 5!5!....5! = 100! / (5!)20

= 1.28 x 10115 (8-8)

The calculation of equation 8-8 assumes that an equal number of each type of amino acid, namely 5, are contained in the polypeptide. Since k, or Boltzmann's constant, equals 1.38 x 10-16 erg/deg, and ln [1.28 x 10115] = 265,

Scr = 1.38 x 10-16 x 265 = 3.66 x 10-14 erg/deg-polypeptide

If only one specific sequence of amino acids could give the proper function, then the configurational entropy for the protein or specified, aperiodic polypeptide would be given by

Scm = k lncm
= k ln 1
= 0
(8-9)
But wait... How does the polypeptide know? In the left hand we have a random polypeptide and in the right a specified one. But there is nothing special about the second one. If I pass them both to you, you cannot tell which is the specified one by doing any sort of experiment. Thermodynamically, they are the same (indeed, they even be the same sequence).

The entropy in both sequences is the same, so clearly Thaxton has got it wrong.

In fact, calculating configuational entropy is far more complex than this, and as this article states, there is no proper way to do it yet.

Tuesday, 19 February 2013

Abusing Thermodynamics: Introduction

For some reason the laws of thermodynamics get particularly abused by creationists. Undoubtedly this is because most of them do not understand them, but a few do, and they should know better. For them, it looks like deliberate deceit. This post introduces the laws, and subsequent pages on this topic will look at the claims of creationists (and one IDist) who hold at least a doctorate and should understand the subject.

There are four laws and, like a C-style array, they are numbered from zero. The important two are the first and second.

The First Law

The first law says that energy (of which matter is one form) is conserved. That is, for any change, the energy at the end of the process is equal to the energy at the start. Now that energy may have moved around or been converted into a different form, but the total overall energy is the same. Mathematically:

E(i) = E(f)

... where E(i) is the initial energy, E(f) is the final energy.

The Second Law

The second law says that entropy (which is a measure of how well spread out energy is) must increase. That is, for any change, the entropy at the end of the process is greater than the entropy at the start. Now that entropy may have moved around, but the total overall entropy must increase. Mathematically:

S(i) < S(f)

... where S(i) is the initial energy, S(f) is the final energy.

A Tendency?

It is worth noting than when you look at individual particles neither law holds, and the Second Law is often described as a tendency. However, at the macroscopic scale the laws are universal - and if it is large enough to see, then it is big enough for the laws to apply.

Energy can be created and destroyed in extremely small amounts for a limted amount of time (see here for more on that), as long as that apparent violation of the First Law is below the limit of the Heisenburg Uncertainty Principle (though there is an alternative way of looking at it).


The Second Law arises because of the magic of big numbers. At the scale of atoms and molecules, entropy can go up or down, but it is statistically more likely to go up. At the macroscopic scale (anything big enough to see), a tendancy in such a vast number of particles has become a certainty. This is the only exception to the Second Law, and I mention it only for completeness. It is not necessary to invoke any such exceptions to explain evolution.

Open and Closed Systems

People often talk about open and closed systems (and sometimes isolated systems too) with regards to these laws. If you have a system that is perfectly insulated so that matter and energy cannot go in or out of it, then energy must be conserved and entropy must increase.

But this is also true in an open system, as long as you consider the overall energy and the overall entropy, and all natural systems are open, so really the distinction is not worth bothering with.

Configurational Entropy, Conformational Entropy and Information Entropy

There are several different types of entropy out there some related to thermodynamics and some not, and often the same name is used either way. In thermodynamics, configurational entropy and conformational entropy are both part of a molecule's total entropy; configurational entropy is the part relating to the arrangement of its atoms, while conformational entropy is the part relating to how a polymer chain is arranged. Information entropy could be a way of looking at thermodynamic entropy (the more spread out the energy, the less you know about where it is, so in a sense information entropy has increased). It is also a legitimate term in information theory - but that does not mean the Second Law of Thermodynamics applies to it.

All three are abused by creationists by applying them to something they should not.

Entropy: An Extrinsic Property

The amount of entropy in a material depends on its state (temperature and pressure essentially) and how much is present; it is an extrinsic property. It does not depend on how the experimenter chooses to measure it. It does not depend on how it got to that state.


For example, 18 g of water (1 mole) at 25°C has an entropy of 69.9 J/K. It does not matter how the water was created or how it got to that state; its prior history is irrelevant (afterall, the water cannot remember what happened). If it is at 25°C and there are 18 g, then it has an entropy of 69.9 J/K. You can see more examples of entropy values here.

The first impotant point here is that if your ideosyncatic method of calculating entropy gets a value different to 69.9 J/K for 18 g of water at 25°C, then your method is nonsense. If it gets different values depending on arbitrary choices in the calculation, then your method is nonsense. Creationists are good at making up new ways to determine entropy, or at least some property that they label entropy, but many of them involve subjective choices in the way the system is examined, and very different results are obtained when it is looked at another way.

The other important point is that thermodynamics does not depend on how it happened. You can determine the overall entropy at the start, you can determine the overall entropy at the end. Has the entropy gone up? If so, the Second Law is being obeyed. How it gets from the start to the end is irrelevant. Creationists are also adept at pretending that the mechanism is relevant; it is not.

Friday, 15 February 2013

Creationists at the Discovery Institute

To be clear, I am considering anyone who denies universal common descent, and believes instead that each "kind" of animal was created separately is a creationist.

There are plenty of people who are creationists and proud of it. The people at "Answers in Genesis" and "Institute for Creation Research" are fine examples. What is of more interest to me are the intelligent design advocates who are also creationists. There is nothing inconsistent about being both an IDist and a creationist, however this does give us some insight into why they might want to promote ID, and why they reject modern evolutionary theory.

Dembski claims that many intelligent design advocates are ex-Darwinists, rather than fundamentalists wanting to promote creationism. However, I have yet to see anything resembling decent argument against common descent, other than reference to a holy book, so I take his words with a liberal pinch of salt:

In my own case, I was raised in a home where my father had a D.Sc. in biology (from the University of Erlangen in Germany), taught evolutionary biology at the college level, and never questioned Darwinian orthodoxy during my years growing up. My story is not atypical. Biologists Michael Behe, Jonathan Wells, and Dean Kenyon all started out adhering to Darwinism and felt no religious pull to renounce it. In Behe’s case, as a Roman Catholic, there was simply no religious reason to question Darwin. In so many of our cases, what led us out of Darwinism was its inadequacies as a scientific theory as well as the prospect of making design scientifically tractable.

We will look at Jonathan Wells in a moment...
You might like to look at a list of fellows of the DI CSC (the ID wing of the Discovery Institute).

Michael Denton and Michael Behe

Michael Denton and Michael Behe both accept universal common descent; they are not creationists. Denton is actually a very interesting case, because originally he rejected common descent. To his credit, when the flaws in his argument were pointed out, he changed his position.


Bruce Chapman

Chapman is the man who founded the Discovery Institute. This comes from a blog post:

At the core of the exhibit is a tiny rodent whom the adorable, if naive, teens are supposed to venerate as their direct ancestor. It cost a lot of money to bamboozle the folks this way. And you taxpayers paid for it.

Stephen Meyer

Meyer is the Program Director at the DI CSC. His CV says he was a "university professor" at Palm Beach Atlantic University from 2002 to 2005. Palm Beach Atlantic University requires all members of staff to believe "that man was directly created by God", so Meyer must be (or have been) a creationist to get that position.

Jonathan Wells

From here:

The problem with universal common descent is not that it conflicts with ID, but that it conflicts with the evidence. In fact, it blatantly distorts the evidence to serve naturalistic philosophy.

Okay, Wells rejects common descent. Now remember that Dembski claims that Wells "started out adhering to Darwinism and felt no religious pull to renounce it"? Wells tells it rather differently:

Father's [Sun Myung Moon's] words, my studies, and my prayers convinced me that I should devote my life to destroying Darwinism, just as many of my fellow Unificationists had already devoted their lives to destroying Marxism. When Father chose me (along with about a dozen other seminary graduates) to enter a Ph.D. program in 1978, I welcomed the opportunity to prepare myself for battle.
- Jonathan Wells, Darwinism: Why I Went for a Second Ph.D.
In fairness to Dembski, Wells tells it both ways!


Dembski

From here:

For the record: I personally don’t believe in common descent though I think there are lines of evidence that suggest considerable evolutionary change. At the same time, there are lines of evidence that suggest considerable discontinuity among organisms. Check out chapter 5 of my forthcoming book with Jonathan Wells titled THE DESIGN OF LIFE (publication date keeps being delayed, but I think it’ll be out in November).

Phillip E. Johnson

From here:

Nowadays I rarely see any attempt to prove that the Darwinian mechanism actually has the power to create major new biological innovations. Instead, the museums and magazines prefer just to tell the story of common descent, assuming that random variation with natural selection (differential reproduction) must have been adequate to perform whatever designing had to be done. At the same time, mainstream science, although guided by Darwinian assumptions, keeps providing more and more evidence of the enormous information content of living structures. Even the core assumption that genetic similarities are necessarily inherited from common ancestors is contradicted almost daily by invocations of something called “lateral gene transfer” to explain genetic similarities between organisms which are not believed to share a recent common ancestor.

Casey Luskin

This whole web page, titled Design vs Descent: A Contest of Predictions, is arguing for design, and against common descent:

Jonathan Witt

Again a whole page arguing against common descent.

Paul Nelson

Dembski says of Nelson: "Nelson’s young earth creationism has been a matter of public record since the mid eighties." Also from here:

I became a fellow at Discovery in 1996, and published a chapter defending YEC with John Mark Reynolds (in the Zondervan volume Three Views on Creation and Evolution) in 1999. In fact, the submission of my chapter MS was delayed, much to the consternation of the Zondervan editors, because Discovery colleagues were urging me to drop out of the book. I've never made any effort to hide my YEC convictions, which are mainly theological in origin.
It is worth noting that most of the DI IDists are old-Earth creationists; he appears to be the only young Earth creationist.

Percival Davis and Dean H. Kenyon

David and Kenyon were the main authors of the text book, Of Pandas and People. Early drafts of this used the term "creationism" instead of "intelligent design" (etc.), and included this statement:

The basic metabolic pathways of nearly all organisms are the same. Is this because of descent from a common ancestor, or because only these pathways (and their variations) can sustain life? Evolutionists think the former is correct; creationists because of all the evidence discussed in this book, conclude the latter is correct

After the creationists lost the Edwards vs Aguillard court case, all references to crationis were removed in the book. Nevertheless this seems adequate evidence that Davis and Kenyon are themselves creationists.

Tuesday, 5 February 2013

When the soul enters the body

An interesting philosophical discuss revolves around the issue of when a human becomes a real person. You could argue that it is not until 18 in a legal sense, as this is the age you can vote, but I guess most people would say an earlier age. How about 10, when you are judged capable of telling right from wrong?

One thing that sets us apart from the beasts is our self-awareness. Perhaps we are only really us once we become self-aware, at 15 to 24 months.

Earlier still? Back in the womb, perhaps, when the brain forms:

Consciousness requires a sophisticated network of highly interconnected components, nerve cells. Its physical substrate, the thalamo-cortical complex that provides consciousness with its highly elaborate content, begins to be in place between the 24th and 28th week of gestation. Roughly two months later synchrony of the electroencephalographic (EEG) rhythm across both cortical hemispheres signals the onset of global neuronal integration.
http://www.scientificamerican.com/article.cfm?id=when-does-consciousness-arise

Traditionally the "quickening" has been considered the important moment. This is when the mother first feels something move

Twenty three weeks is consider the age of viability, which fits with the above; babies born after this time have a fair chance of surviving.

The fact that babies can survive after such an early birth makes the birth itself a dubious cut-off point. There is a huge developmental difference between a baby born at 23 weeks and one born at full term, and the former will have to spend a long time in an artificial womb (which is what a neonatal intensive care unit effectively is).

It is a question that has no simple answer; the reality is probably that it is an on-going process, and any arbitrary cut-off will be unsatisfactory.

Abortion

Now let us throw religion into the mix. The Christian Right have decided that abortion is wrong (personally, I am not sure either way; as I said, there is no simple answer). Having decided abortion is wrong, they then need to twist the Bible to rationalise their opinion, and to force it on others. They have been fairly successful in the US; abortion is still legal, but the foetus now has rights too, as of 2003.

That is a big step to getting abortion illegal, and furthermore ensuring it never gets legalised in the future.

What is interesting to me is how these Christians twist the Bible to serve their needs. This is a web site about creationism first and foremost, but those same people who reject evolution because it contradicts the Genesis account are happy to ignore what the Bible says when it comes to abortion.

Scripture

The Bible has little to say directly. A verse in Exodus appears to offer some support to anti-abortionists:

Exodus 21:22 “When men strive together and hit a pregnant woman, so that her children come out, but there is no harm, the one who hit her shall surely be fined, as the woman's husband shall impose on him, and he shall pay as the judges determine. 23 But if there is harm,[d] then you shall pay life for life, 24 eye for eye, tooth for tooth, hand for hand, foot for foot, 25 burn for burn, wound for wound, stripe for stripe.

However, this relies on a mistranslation. If the woman miscarries, the man who hit her is fined, but not punished as though this was an actual person, as the  anti-abortionists would have us believe. The "life for a life" sentiment is for the mother not the unborn. The mother is a person, and the normal rules apply. the unborn is not a person; the mother receives some financial compensation only.

Spirit and Breath

To the ancient peoples, spirit and breath were one and the same.

Genesis 2:7 Then the Lord God formed a man[c] from the dust of the ground and breathed into his nostrils the breath of life, and the man became a living being.

God brings Adam to life by breathing on him, giving him spirit.

Several times in the Bible the expression "giving up the ghost" is used when someone dies. In Hebrew, it actually says dying breath. For the Biblical author, breathing was what defined life; when the breath was gone, life was gone (eg see discussion here).

Genesis 25:8-9 Then Abraham gave up the ghost, and died in a good old age, an old man, and full of years; and was gathered to his people. And his sons Isaac and Ishmael buried him in the cave of Machpelah

Genesis 35:29 And Isaac gave up the ghost, and died, and was gathered unto his people, being old and full of days: and his sons Esau and Jacob buried him

Genesis 49:33 And when Jacob had made an end of commanding his sons, he gathered up his feet into the bed, and yielded up the ghost, and was gathered unto his people

For Biblical translators, they equated the dying breath with the spirit (or ghost). When you give your last breath, your soul comes out with it; the reverse of what happened to Adam. But this happened to people who were born of the womb too, not just Adam.

In fact the English word "spirit" comes from the Latin for breath, "spiritus". In Greek the word "pneuma" means breath, but also means spirit (we get words like pneumatic and pneumonia from it). See also this concordance relating breath to spirit for the Hebrew word "ruach".

It is a fact that in the ancient world breath and spirit were literally synonymous.

The Holy spirit that hovers above the waters right at the start of Genesis? That is the breath of God. So no wonder Adam comes alive when God breathes on him! But the breath is also the spirit, and at that moment Adam also receives a spirit.

A couple more illustrative verses:

Job 33:4 The spirit of God has made me, and the breath of the Almighty gives me life.

Ezekiel 37:5 This is what the Sovereign Lord says to these bones: I will make breath[a] enter you, and you will come to life.

We lose sight of this because we have separated breath and spirit into two different concepts, but that is just our modern perspective. To the ancients, they were the same. While you breathed you had a spirit; when you died, you let out your dying death, and your spirit departed - you gave up the ghost.

Now I appreciate the Bible is not explicit, but the natural consequence of this is that the spirit enters the body when the baby takes his first breath.

What the Christians say

Christians dredge up all sorts of nonsense from their holy book to support their claims. Here are a few verses I have seen cited.

The first one is interesting as it gets translated two quite different ways.

Psalm 51:5 Behold, I was shapen in iniquity; and in sin did my mother conceive me.

Psalm 51:5 Surely I was sinful at birth, sinful from the time my mother conceived me.

It is tempting to just quote the first, and say that the Psalmist refers to a sin perpetrated be his mother and/or father when he was conceived. However, I think the real point here is that the Psalmist is saying that he is so wicked that he must have been made that way. Christian will often say man has a sinful nature, and the Psalmist here is saying that he has a downright wicked nature.

Surely no one can believe he was actually sinning from the moment of conception?

Psalm 139:13 For you created my inmost being;
you knit me together in my mother’s womb.
14 I praise you because I am fearfully and wonderfully made;
your works are wonderful,
I know that full well.
15 My frame was not hidden from you
when I was made in the secret place,
when I was woven together in the depths of the earth.

This is about the physical body developing in the mother. We all know that happens. It does not indicate that the foetus had a spirit while this was happening.

Jeremiah 1:5 “Before I formed you in the womb I knew[a] you,
before you were born I set you apart;
I appointed you as a prophet to the nations.”

This refers to a time before conception. Either you have to claim that babies have spirits even before they are conceived or this verse cannot support the claim that the foetus is alive.

Genesis 25:22 And the children struggled together within her; and she said, If it be so, why am I thus? And she went to enquire of the Lord.
23 And the Lord said unto her, Two nations are in thy womb, and two manner of people shall be separated from thy bowels; and the one people shall be stronger than the other people; and the elder shall serve the younger.

This is a story about a woman pregnant with twins who kick a lot. It would seem that the Christian belief is that these unborn babies are actually fighting each other in the womb, one trying to dominate the other in anticipation of the day that they will rule separate nations. A rather simpler explanation is that this was God telling her she had twins, so expect a lot of kicking, and by the way, this is what I foretell for them.

Luke 1:41 When Elizabeth heard Mary’s greeting, the baby leaped in her womb; and Elizabeth was filled with the Holy Spirit.

I have to acknowledge this is the best one. However, the Bible makes it clear that this was an exception:

Luke 1:15 For he shall be great in the sight of the Lord, and shall drink neither wine nor strong drink; and he shall be filled with the Holy Ghost, even from his mother's womb.

Some commentary on that verse, both from here.

"Shall be filled with the Holy Ghost - Shall be Divinely designated to this particular office, and qualified for it, from his mother's womb - from the instant of his birth. One MS., two versions, and four of the primitive fathers read εν τῃ κοιλιᾳ, In the womb of his mother - intimating that even before he should be born into the world the Holy Spirit should be communicated to him. Did not this take place on the salutation of the Virgin Mary? - and is not this what is intended, Luke 1:44? To be filled with the Holy Ghost, implies having the soul influenced in all its powers, with the illuminating, strengthening, and sanctifying energy of the Spirit."

"and he shall be filled with the Holy Ghost, even from his mother's womb; or "whilst in his mother's womb", as the Syriac, Arabic, and Persic versions render it: like Jeremiah, he was sanctified, set apart, and ordained to be the prophet of the Highest, before he came out of his mother's womb; and was then under such an influence of the Spirit of God, as to leap in it for joy, at the salutation of the mother of Christ to his, Luke 1:41 and very early appeared to have the extraordinary gifts and graces of the Holy Ghost, qualifying him for his work,"

I presume people already appreciate Jesus' situation was unique.

At best verse in Luke supports the claim that the soul enters the body at some point during pregnancy; it offers no support to the claim that a fertilised egg has a soul.

Further thoughts

It is interesting to read this:

Exodus 23:26 “There shall be no one miscarrying or barren in your land; I will fulfill the number of your days.”

Hosea 9:14 “Give them, O Lord-- what wilt Thou give? Give them a miscarrying womb and dry breasts.”

It would seem as if God is responsible for whether a foetus miscarriages or not. Estimate vary from 30% to 50% of preganancies ending in miscarriage (the vast majority without the mother realisibng she was pregnant). All those poor innocent babies he chooses to murder...

Or maybe not. The ancient Hebrews would not have considered them individuals because they did not have breath/spirit. It is just the modern Christian, who ignores what the Bibles say, and so has to content with this dilemma.

This is an article by Henry Morris III, of the Institute for Creation Research. The point of the article is to establish that plants are not alive. His argument is that they are not "chay", the Hebrew for alive, and then gives some characteristics of "chay". One in particular is of interest:

Life has independent movement.

This may seem like either an obvious point or an irrelevant one. However, one of the descriptive terms that the Creator applied to living creatures was “movement.” The Hebrew word is ramas, used 17 times in the Old Testament—never about plants or vegetation of any kind. Living things move.

And living things eat plants! Plants do not travel from one location to another, except on the backs of animals, blown on the wind, or transported by men. They are “rooted.” They do not have the power of ramas. Living things have the ability to move independently, but plants do not.

A foetus does not have independant movement, and so is not "chay", and would not be considered alive (in this Hebrew sense of the word anyway). There is, then, an important difference in quality between the foetus (not chay) and the adult (chay) for the Biblical authors.

Again and agan the Bible is telling us that a baby does not have a spirit, is not a proper person, until it takes its first death. Christians choose to ignore what their holy book says because it does not coincide with their opinion on abortion.