Information in the Genome

Many times I read that there is no evidence that evolutionary mechanisms have added information to a genome. Recently this claim was reproduced on a blog post titled Entropy, Evolution or De-Evolution.

The entire post is filled with misunderstandings and misrepresentations. I wanted to focu on one of the claims reproduced there. The claim is attributed to Bruce Malone, though no further information is given concerning it. Malone apparently has a Bachelors in Chemical Engineering, though no relevant expertise regarding evolutionary biology.

The quote is as follows:

No experiment has ever shown how useful functioning information can be added to the DNA molecule by random changes.

I have tried to track down the souirce of the quote so I can see it in context, but have not found it as yet.

Here, Bruce Malone claims that DNA changes don't result in any additional "useful functional information". No definition of what this might be is given. In the absence of any definition, we can look to the field of Information Theory.

As I understand it, by any measure of information as understood within Information Theory, taking 2 identical strands of DNA, and then changing one of them results in an increase in information. It doesn't matter if this is a change of a single base pair, and it doesn't matter if this change would result in a beneficial, detrimental or neutral result in the organism.

How about "complex specified complexity" or "specified complexity", a term coined by Intelligent Design proponent William Dembski. He defines it as a property of organisms that cannot have arisen through natural processes, and that must have arisen through the actions of an intelligent agent. However, it's been shown that evolutionary mechanisms can produce "information" in this sense, and that repeated application of these mechanisms can produce sufficient information to cross Dembski's claimed "Universal Probability Bound". Dembski's ideas have been found to be without merit. As a brief example, researchers in the field of Artificial Life, where computer simulations are used to study evolutionary mechanisms, all ostrs of novelties and increased complexity are observed which should be impossible were Dembski's claims correct.

What about "functional information", as proposed by Stephen Meyer. Meyer defines this as the production of linear sequence-specific arrangements of characters. He states that it is our uniform experience that this sort of information only arises with the actions of an intelligent agent. There's no doubt that we, as the main intelligent agents we are aware of, can create this sort of information. However, Meyer's leap from this to the conclusion that an intelligent agent is necessary for these sorts of strings of symbols (as we could view DNA) is not valid. In fact, as was mentioned above when discussing Dembski's "specificed complexity", evolutionary mechanisms can and have generated this information.

So that would mean that Malone must be using "useful functional information" to refer to something else. Whatever it is, I can guess that it's either a useless concept, or the claim that evolutionary mechanisms cannot account for it is false.

The myth of Christian persecution & discrimination in the USA

Reading through blogs and articles from Right Wing Christians, the claim of increasing discrimination an persecution of Christians seems to be a common theme. Claims of rampant "secularism" eroding the rights of Christians to practice their beliefs, or voice their opinions.

As a secular athiest on more on the Liberal/Left side of the political spectrum, I have to say that I really don't see merit to the claims being made.

A recent example is a Bakery in Colorado which refused to provide a cake for a same-sex wedding on the basis of the proprieters religious beliefs. The propieter is arguing that baking a cake is a form of expression, essentially speech, and therefore being compelled to bake a cake for an event that goes against their (sinerely held) religious beliefs is a violation of their first amendment rights. The state of Colorado is arguing that refusing to bake the cake is in violation of the public accomodation laws, under which facilities which are open to the public may not discriminate on the basis of race/color, sex/gender, ancestry or national origin, marital status, sexual orientation, or gender identity.

The bakery is obviously a public facility, and it seems obvious that religious belief here is being used to avoid anti-discrimination laws. I don't see that the proprieter would get much traction if they were arguing for the right to discriminate against one of the other classes of people protected under the public accommodations law. If we substitute african americans, or an interacial couple, or women, or unmarried couples for same-sex couple, it sems obvious that the bakery has no right to refuse service in this case.
It seems to me that the bakery is arguing for the right for anyone to discriminate against anyone else, for (almost) any reason, as long as its because of "sincerely held religious beliefs". Does anyone actually want that? I doubt it.

Misunderstanding thermodynamics

A recent blog post claims that thermodynamics supports the conclusion that God exists. Unfortunately, the author misunderstands thermodynamics, implying that things like evolutionary biology aren't compatible with the second law of thermodynamics, and that the universe began in "perfection" and has been going downhill ever since.

The authors confusion and misunderstandings are understandable given a source he cites titles De-Evolution. This article makes the following claim:

This idea is completely contradicted by the Second Law, which stipulates that all real “systems and processes” including all biological and physical processes, naturally diminish to lower levels of organization and complexity—regardless of whether the system is open or closed.11 According to Dr. R. B. Lindsay, Ph.D. in physics, the Second Law reveals that the “natural tendency of complex, ordered arrangements and systems is to become simpler and more disorderly with time.”12 In summary, there is an irreversible downward trend at work throughout the universe.

The above quote, reproduced in the blog post which inspired me to write this, makes a hash of thermodynamics and the concept of entropy. It fails to take into account the obvious fact that while entropy tends to increase over time in a closed system, there is no reason why parts of that system cannot see increases in order/complexity, and decreases in entropy. After all, the entropy of a system can be reduced from outside of it by the introduction of energy. For evolutionary biology, this energy is predominantly from the sun.

The author of the blog post make a claim that the universe began in perfection (or near perfection) and has degraded ince then:

Therefore, the findings of entropy align with the biblical account that God had created the universe and described it as “very good,” and it has been going downhill since.

This statement also misunderstands science. The universe, at the moment of the big bang event, was in a state of maximal entropy. So, in contrast to starting in a state that was "very good", the universe started out in a state the author might characterize as "very bad".

If the universe started out in this state of maximal entropy, how is it that the universe has ordered structures in it now? Shouldn't it be that case that once a system hits maximal entropy, it will stay in that state (also called equilibrium)? No, not if the maximal entropy possible in that system is increased, which is exactly what has heppened with our universe. The expansion of the universe has increased the maximum potential entropy of our universe far more rapidly than the abolute entropy of our universe has increased. This has resulted in an "entropy differential" if you will, a gap between the current entropy and the maximum entropy possible in the universe, and it's this which has made it possible that structure has formed while the absolute entropy of the universe continues to increase. If creationists like the author of the inspirational blog post, and the author of the "De-Evolution" piece presented the science as it's actually understood by scientists instead of presenting misinformation and miunderstandings, I'm sure I would have far fewer complaints about their claims.

Do scientists and Philosophers convert based upon the arguments and evidence?

A recent blog post concerning Evidence that God Exists, the author quotes scientist Alan Sandage in support of the contention that the evidence of science supports the conclusion that God exists. The same author has on other occasions referred to Anthony Flew, whose (near) death bed conversion to Deism is also referenced in support of the same contention.

Are these examples of conversion to beliefs in a God (of a sort) examples of scientists and philosophers converting due to the evidence?

Trivially, the answer is yes. In both of these cases, the person in question cites some scientific evidence (in both cases it's the complexity of biochemistry/DNA).

If we look a little closer, and think about the way in which these examples are being used, which is that these people are experts and they ere convinced by the evidence, then we can see that these examples should be taken with a grain of salt.

Both of these people are experts in their respective fields, which are Cosmology in the case of Sandage, and various areas of Philosophy for Flew. Neither of these two men appear to have relevant expertise in the area of science they cite to support their conversion claims. This means that these are NOT examples of experts that were converted by the evidence. Their conversion stories should be given no greater weight than that of Joe Bloggs down the road who read a book on biology and came to the same conclusion.

The examples which should be produced are those where someone was convinced by the evidence in their field of expertise that a God or Gods exists. I can think of a single example of this - Edwards Feser - who states that he was convinced to convert to Catholicism by the Cosmological Argument (the Thomistic rather than Kalam variant).

In contrast to this, I suspect there are a vast number of people who were convinced to become Deists or Agnostics or Atheists while studying to become experts in their field, especially considering the inverse correlation between increased education and religious belief.

I would love to hear about more examples of experts who were convinced by the evidence in their field to become theistic.

Is God the only basis for objective morality?

Just a couple of quick references to critiques of Divine Command metaethics (DCM), which show that there can be other objective foundations for morality, and that basing morality upon God isn't successful.

In "In defense of non-natural, non-theistic moral realism", Erik Wielenberg argues that there are ethical brute facts which supervene on "states of affairs". Wielenberg notes that DCM proponents find these sorts of "freely floating" ethical facts to be weird, and then points out that these people are also committed to these "strange" ethical brute facts:

• P1) Part of the definition of God is the statement "God is Good"
• P3) "God exists" is a brute fact
• P4) From P2, "God is Good" is a brute fact
• P5) "God is Good" is an ethical statement
• C) from P4 & P5, "God is Good" is an ethical brute fact

In "A sematic attack on Divine Command Theory", Stephen Maitzen argues that Divine Command Metaethics is either vacuous, or false, starting from the uncontroversial DCM statement "For any agent x, x is morally good because, and only to the extent to which, x wills what God wills": true

P1) The statement "God is Good" is not religiously trivial P2) Every tautology (eg. "Good is Good", "God is God") is religiously trivial P3) If 2 statements have the same meaning, then one is a tautology only if both are P4) According to DCM, "X is Good" has the same meaning as "X wills what God wills" P5) From P4, the statement "God is Good" has the same meaning as "God wills what God wills" P6) "God wills what God wills" is a tautology P7) From P3, P4, P%, according to DCM "God is Good" is a tautology P8) From P2, P7, according to DCM, "God is Good" is religiously trivial P9) From P1, P8, DCM is incompatible with traditional theism P10) From P9, if traditional theism is true, DCM is false P11) If moral nihilism is false and DCM is true, then traditional theism is true P12) From P11, if traditional theism is false, then moral nihilism is true or DCM is false P13) From P12, if traditional theism is false, then DCM is true only if moral nihilism is true P14) Traditional theism is true, or traditional theism is false C) From P10, P13, P14, DCM is true only if moral nihilism is true

Read the papers themselves for more detailed arguments and justifications of the claims.

Why so certain?

I've heard from a number of Christians that there is no possibility of them changing their views. That I am wasting my time in even trying to discuss it with them. This seems to me to be a fairly counter productive position to take, and seems almost designed to stop further conversation. Even accepting that, however, I still find that I want to know why this person is so certain. What is so convincing that the person is willing to state, unequivocally, that nothing could change their mind. So, what is the answer? That's what this post is for - you tell me. Educate me as to why you have such certainty. Theists and atheists alike (and agnostics, and anyone in between) - if you are certain of your position, and/or believe you could not be argued out of it, explain why? Or, tell me of reasons you have heard from others, regardless of their beliefs.

Was Biblical slavery "OK"?

This post is a response to Biblical Slavery vs Other Forms, which is a horrible apologetic for slavery.

Slavery as an institution

Today slavery is admitted to be an immoral institution. The owning of another person, and the treatment of that person as mere property is fairly obviously wrong to us today. It is bad for society, as it results in a permanent underclass. It is a result of inconsistent application of reason to the moral realm.
Christians will join in this chorus of voices in denouncing slavery. Many of them will also agree that slavery has always been immoral, and that the bible was simply mistaken to advocate it. Some Christians, however, will argue that biblical slavery was somehow different, was somehow moral, and therefore somehow a-ok. This is an ad-hoc claim made due to their ideological commitment to inerrancy rather than a rational review of the institution of slavery as ownership of another person, as well historical revisionism applied to the manner in which slavery has been practised in the past.
Christians who are obliged to make an apology for slavery based upon their commitment to biblical  inerrancy also tend to make claims regarding the objective, absolute and unchanging nature of morality. This appears to be an incoherent position to hold, assuming they admit that slavery is immoral today.
I am not aware of anyone who argues that slavery should be legal and encouraged, though this appears to be the position which is consistent with an apologetic for biblical slavery. I suspect that these people would be unwilling to admit that slavery is a moral institution and should be practised.

Slavery in the Old Testament

To acurately assess the "specialness" of biblical slavery we should not be comparing it to New World slavery. We should be comparing it to other laws of the time and region. For example, biblical slavery's concept of release in a Jubilee year is often held up as being laudible. Let as look at this, and compare it with a similar law.
First the bible:

Deut 15:12 "[And] if thy brother, an Hebrew man, or an Hebrew woman, be sold unto thee, and serve thee six years; then in the seventh year thou shalt let him go free from thee." KJV

We can see that the biblical code relating to debt slavery above only applies to those who were Hebrew prior to being sold, and only when the Hebrew is sold to another Hebrew.
Now, let's compare this with the Code of Hammurabi.

Code of Hammurabi passage 117 "117. If any one fail to meet a claim for debt, and sell himself, his wife, his son, and daughter for money or give them away to forced labor: they shall work for three years in the house of the man who bought them, or the proprietor, and in the fourth year they shall be set free."

We can see that not only does this code halve the length of servitude, but it applies to any and all people who become slaves through paying a debt.
We can easily see here, that the bible is not particularly "special" in it's time and place.

When we look at biblical slavery in context we see that it is similar to, and often times worse than slavery in the surrounding nations.

Let us look at the claimed human treatment accorded to slaves in the bible.

Exodus 21:20-12,26-27 "And if a man smite his servant, or his maid, with a rod, and he die under his hand; he shall be surely punished. Notwithstanding, if he continue a day or two, he shall not be punished: for he [is] his money. ... And if a man smite the eye of his servant, or the eye of his maid, that it perish; he shall let him go free for his eye's sake. And if he smite out his manservant's tooth, or his maidservant's tooth; he shall let him go free for his tooth's sake. KJV

We can see from this that slaves are treated as property. Slave owners were allowed to beat their slaves with relative impunity. The only punishment which could occur is if the slave died staright away, or if they were rendered unfit (losing an eye or a tooth). We notice that there is no injunction against beating slaves here, as would be expected of a human code (in fact, a human code would simply make it clear that slavery was immoral/illegal).
Another passage also deserves comment:

Leviticus 25:48 "And if a sojourner or stranger wax rich by thee, and thy brother [that dwelleth] by him wax poor, and sell himself unto the stranger [or] sojourner by thee, or to the stock of the stranger's family: After that he is sold he may be redeemed again; one of his brethren may redeem him: Either his uncle, or his uncle's son, may redeem him, or [any] that is nigh of kin unto him of his family may redeem him; or if he be able, he may redeem himself. And he shall reckon with him that bought him from the year that he was sold to him unto the year of jubile: and the price of his sale shall be according unto the number of years, according to the time of an hired servant shall it be with him." KJV

In this passage we can see that this only applies to Hebrew's who are sell themselves to foreigners. This is quite a restricted condition, and certainly does not apply to Hebrews who sell themselves to other Hebrews, Hebrew slaves from birth, or foreigners.
It is often claimed that foreigners who were slaves to Hebrews could simply convert and enjoy the benefits of release in the Jubilee year. This is not as obviously easy as some would maintain however.
For example, most of the restrictions on slavery that apply to Hebrew's apply to those who were considered Hebrew's prior to becoming slaves. There does not seem to be any evidence that a convert would be treated as a life long Hebrew in these circumstances. There are also groups of people to whom conversion was unavailable. Eunuchs, Moabites, and others were not ever to be allowed into the convenant with Yahweh. There is also the immorality of requiring conversion in order to be treated humanely. The author of the blog who inspired this has often complained of the poor treatment of Christians in Muslim nations. This poor treatment could be alleviated by these Christians converting to Islam. I doubt the author would approve of this course of action, nor would he consider this a moral system, and yet he is endorsing exactly the same sort of behaviour as moral. This amounts to special pleading on behalf of biblical slavery.

Slavery in the New Testament

If we look in the New Testament for passages denouncing slavery, we will be very disappointed. We find many passages exhorting slaves to be obedient to their masters:

Ephesians 6:5 Slaves, obey your earthly masters with respect and fear, and with sincerity of heart, just as you would obey Christ. NIV

Colossians 3:22 Slaves, obey your earthly masters in everything; and do it, not only when their eye is on you and to curry their favor, but with sincerity of heart and reverence for the Lord NIV

1 Timothy 6:1-2 All who are under the yoke of slavery should consider their masters worthy of full respect, so that God’s name and our teaching may not be slandered. 2 Those who have believing masters should not show them disrespect just because they are fellow believers. Instead, they should serve them even better because their masters are dear to them as fellow believers and are devoted to the welfare[a] of their slaves. These are the things you are to teach and insist on. NIV

Titus 2:9-10 Teach slaves to be subject to their masters in everything, to try to please them, not to talk back to them, and not to steal from them, but to show that they can be fully trusted, so that in every way they will make the teaching about God our Savior attractive. NIV

1 Peter 2:18 Slaves, in reverent fear of God submit yourselves to your masters, not only to those who are good and considerate, but also to those who are harsh. NIV

We can see from this selection of passages that slavery was to be accepted. There is no hint that slavery as an institution was immoral, and Christian slaves were to submit to masters regardless of how cruel or kind, whatever their beliefs. These are not the writings of those who believed slavery to be immoral, as we can see in the following verse, directed at slave owners:

Ephesians 6:9 And masters, treat your slaves in the same way. Do not threaten them, since you know that he who is both their Master and yours is in heaven, and there is no favoritism with him. NIV

We see here the master asked to treat his slaves well. Not to set them free, as we would expect were slavery considered immoral by the author. It also likens God/Jesus to a slave master, an interesting observation in it's own right, given the frequent image portraying God as a loving father. The following passage from 1 Timothy, has been presented as denouncing slavery:

1 Timothy 1:10 "for the sexually immoral, for those practicing homosexuality, for slave traders and liars and perjurers—and for whatever else is contrary to the sound doctrine" NIV

We are informed that the denunciation of slave-traders is a denunciation of slavery generally. However, the word translated as "slave-traders" - "andrapodistes",  more correctly means one who unjustly reduces free men to slavery, or who steals the slaves of another. The NIV appears to be attempting to soften the message. The KJV renders this term as "manstealers" for good reason. It is obvious that this is not a condemnation of slavery, but rather of kidnapping and theft of property.

The letter to Philemon is another example of the NT condining slavery. Paul is sending the slave Onesimus, back to Philemon. While Paul implies that he would like Philemon to release Onesimus, or perhaps to buy his freedom through the debt Philemon owes to Paul, not once does Paul say that slavery is immoral, nor claim that Philemon should release a fellow brother.

Perhaps one might argue that it was dangerous to argue against slavery at this time, and that the NT authors were simply working within the strictures forced upon them.
This is not a satisfactory explanation for the endorsements of slavery by the New Testament authors for (at least) 2 reasons.

Firstly, there were those who did argue for the freedom of slaves. Tacitus, in his Annals (4.27) relates the story of one such person, Titus Curtisius.

Annals 4.27 The same summer, the germs of a slave war in Italy were crushed by a fortunate accident. The originator of the movement was Titus Curtisius, once a soldier of the praetorian guard. First, by secret meetings at Brundisium and the neighbouring towns, then by placards publicly exhibited, he incited the rural and savage slave-population of the remote forests to assert their freedom. By divine providence, three vessels came to land for the use of those who traversed that sea. In the same part of the country too was Curtius Lupus, the quaestor, who, according to ancient precedent, had had the charge of the "woodland pastures" assigned to him. Putting in motion a force of marines, he broke up the seditious combination in its very first beginnings. The emperor at once sent Staius, a tribune, with a strong detachment, by whom the ringleader himself, with his most daring followers, were brought prisoners to Rome where men already trembled at the vast scale of the slave-establishments, in which there was an immense growth, while the freeborn populace daily decreased."

With the claims of Christians that the apostles were martyred for what they believed, indicating that principle was more important than the consequences to these people, their endorsement of slavery becomes all the more damning.

We can also compare the New Testament endorsements with another contemporary, Musonius Rufus, who while falling short of arguing for the freeing slaves, did go much closer to this than any of the New Testament authors did. Musonius Rufus, a Stoic Philosopher who lived between 30AD and 100AD, taught that "one should endure hardships, and suffer the pains of labor with his own body, rather than depend upon another for sustenance", indicating that we should not live from the labour of slaves. He also regarded forcing sex from slavegirl as immoral, comparing them to free women. Most amazingly, in a time when agitating against slavery would get you killed in short order, Musonius argued that it was right to disobey an unlawful/immoral command from any superior, whether they be a father, magistrate, or owner. This stands in stark contrast to the endorsement of slavery we find in the NT, and is an indictment against the moral standing of those authors and their writings.

We can see that not only does the New Testament not decry slavery as immoral, but actively endorses it. At best, the New Testament asks slave owners to treat their slaves with kindness.
We can also see that non-Christians were willing to argue more closely the immorality of slavery, and in cases were martryed for their beliefs in the immorality of slavery.

New World slavery

I'll only speak a little about New World slavery, as practiced in the America's. Though it is often used as the contrast against which biblical slavery is shown in a favourable light, such a comparison is not appropriate for a number of reasons.
Firstly, New World slavery is far removed both culturally and temporally, from biblical slavery. As I've demonstrated above, biblical slavery, when compared with it's contemporaries no longer looks favourable.
I've also noted that the institution of slavery itself, of owning another person, is immoral on the face of it. If this is the case, then regardless of how favourable biblical slavery is when compared with some other form of slavery, it is still immoral, and so such comparisons do nothing to rescue biblical slavery.
And finally we can note that the culture which gave rise to New World slavery was thoroughly Christian. Christians instituted it, Christians practised it, Christians opposed it's abolition.
Since, as I've demonstrated above, the Christian bible is pro-slavery, the anti-abolitionists used strong scriptural arguments in support of slavery which were unavailable to the abolitionists. Although many prominent abolitionists were Christians, their opposition to slavery was in spite of, rather than because of, Christianity.

UPDATE: Just stumbled upon a quote from the Governor of South Carolina in 1844, concerning slavery:

It is impossible therefore to suppose that slavery is contrary to the Will of God. It is equally absurd to say that American slavery differs in form or principle from that of the chosen People. We accept the Bible terms as the definition of our slavery and its precepts as the guide of our conduct. We desire nothing more. Even the right to buffet which is esteemed so shocking finds its express license in the Gospel (1 Peter ii 20). Nay what is more, God directs the Hebrews to bore holes in the ears of their brothers to mark them when under certain circumstances they become perpetual slaves (Ex. Xxi: 6). I think then I may safely conclude and I firmly believe that American slavery is not only not a sin but especially commanded by God through Moses and approved by Christ through His Apostles.

Notice the support he draws from the Bible, not just for the institution of slavery, but for beating your slaves:

1 Peter 2:20 But how is it to your credit if you receive a beating for doing wrong and endure it? But if you suffer for doing good and you endure it, this is commendable before God.

Conclusion

As this brief foray into the relationship between Christianity and slavery shows, the bible, and bible based Christianity is actually pro-slavery. Modern Christians who are ant-slavery hold this position in spite of their holy book, not because of it. The "moral zeitgeist" has moved on and many Christians have rationalised their beliefs to accommodate this. As we can see, however, both the books of the Old Testament and the New Testament do not denounce slavery, and actively support the institution. This puts Christians who believe the bible is without error in the position of either holding contradictory beliefs - that slavery is both immoral and moral, or in the position of supporting slavery today, and there do not appear to be many in the latter camp. Those mounting an apologetic for biblical slavery ought to feel ashamed of themselves. Unfortunately they often come across as pleased with their work.

A thorough refutation of biblical slavery, among other things, written by Thom Stark is available here. This is a response to Paul Copans apology for biblical genocide and slavery "Is God a Moral Monster?"