Friday, December 28, 2012

Is Intelligent Design theory a science stopper? The ENCODE project

The Intelligent Design theory of life on Earth has been labeled a “science-stopper” by some who believe in a purely naturalistic evolutionary beginning and development of living organisms. The assertion accuses ID theorists of invoking a supernatural cause to natural processes that are not well understood. Is that true? Ardent atheist Richard Dawkins, wrote in his influential 1976 book The Selfish Gene, that non-coding DNA functioned like a “parasite” within the genome. In the evolutionary process, these useless segments of the genome remained after fulfilling their function, raising the question, according to Dawkins, of why a creator would insert worthless code into a genome. Even Francis Crick, Nobel Prize winner and co-founder of the double helical structure of DNA, in 1980, dismissed most of the genome as “little better than junk”. He continued by predicting that it would be “folly” for scientific researchers to “hunt obsessively” for function for many sections of DNA. [1]

Beginning in 2003, the National Human Genome Research Institute initiated an ambitious project named ENCODE, the Encyclopedia of DNA Elements, with the goal of identifying functional elements in the human genome sequence. The ENCODE project continued where the Human Genome Project left off. The first phase concluded in 2007 and the results of the second phase were released on September 15, 2012 in the form at least 30 papers published in several scientific journals (Nature, Genome Biology, and Genome Research). After $185 million, research by 32 groups involving more than 440 scientists, the consortium has discovered function for roughly 80% of the genome, including more than 70,000 “promoter” regions where proteins bind to control gene expression. They have also identified almost 400,000 “enhancer” regions which regulate expression of distant genes. [2] Researchers mapped more than 4 million regulatory regions where proteins interact with DNA. They performed more than 1,600 sets of experiments, using state of the art DNA sequencing technologies, generated more than 15 trillion bytes of raw data and consumed the equivalent of more than 300 years of computer time for analysis. [3]

The researchers found that, though only a small amount of genome directly manufactures messenger RNA for protein-coding, much of the DNA becomes transcribed into non-coding RNA molecules, some of which regulate gene expression. This critical function can operate to turn on or turn off certain portions of the genome. In the past, these segments were often called DNA deserts or “junk DNA”, because they did not appear to have any useful function. In 2000, when the Human Genome Project presented its first rough draft of the sequence of bases, the initial results seemed to confirm evolutionary theory that perhaps 97 percent of the 3.2 billion bases had no apparent function. About 1.2% of the genome bases were found to be involved in protein-coding, which was somewhat expected. However, the ENCODE project found about 8-9% of the bases were involved in regulation. According to computational biologist and project manager Ewan Birney, “One can use the ENCODE data and come up with a number between 9 and 80 percent” attributable to functional significance. [4] It could take decades to fully analyze and comprehend the raw data, but results at this time clearly indicate that vast portions of DNA previously considered to be useless are indeed useful.

Eric D. Green, M.D., Ph.D., director of the National Human Genome Research Institute (NHGRI) stated: “"During the early debates about the Human Genome Project, researchers had predicted that only a few percent of the human genome sequence encoded proteins, the workhorses of the cell, and that the rest was junk. We now know that this conclusion was wrong." [3] While naturalistic Darwinian theorists essentially considered these regions to be the molecular equivalent of a human appendix – useless leftovers from our evolutionary past – intelligent design proponents asserted that function could be discovered for most or all of these. So, which theory would have been considered more of a science-stopper just a few years ago? Rather than an alleged God-of-the-gaps, “junk DNA” could logically be considered evolution-of-the-gaps reasoning.

Biochemist Dr. Fazale Rana notes that “researchers are uncovering more and more examples of the functional importance of junk DNA. In light of this ongoing advance, it is becoming harder and harder to maintain that genomes are riddled with useless evolutionary vestiges.” [5] Even more intriguing, the methods of data organization within DNA are uncannily similar to those utilized in digital data storage by humans today. Stephen C. Meyer, PhD, University of Cambridge, noted that the hierarchical layering within the genome allow for vast amounts of data storage: “The functions they perform are so strikingly similar to functions that we’ve designed to solve similar information and storage problems in high tech digital computers.” [6]

Rather than applying the brakes to scientific discovery – a common accusation - belief in God and Christianity in particular was the impetus for the greatest expansion of knowledge and discovery throughout much of history. Of the major world religions, Christianity is based on reason, giving rise to exploration of logical physical laws of the universe and a rational creator. A very short list of scientists who have made critical discoveries while holding to a strong Christian faith were: Johannes Kepler (laws of planetary motion), Isaac Newton (mathematics), Nicholas Copernicus (astronomy), Francis Bacon (experimentation and inductive reasoning), Robert Boyle (gas laws), Michael Faraday (electricity and magnetism), William Kelvin (modern physics), Max Planck (quantum theory), and Gregor Mendel (mathematical foundations of genetics). Some additional 20th century Nobel prize winners in the sciences with a strong faith in God include: Werner Heisenberg, Erwin Schroedinger, Gugleilmo Marconi, and Arno Penzias. [7]

The discovery of function in regions of the human genome that were previously thought to be useless leftovers from our evolutionary past further illustrates the fact that belief in an intelligent creator is not a science-stopper; on the contrary, it provides the philosophical impetus to uncover the intricacies of the creation. Other examples could be cited, such as the big bang theory. Prior to Georges LeMaitre and Albert Einstein’s discoveries that the universe is indeed expanding, the prevailing understanding of the cosmos was that of a steady state, with no discernible beginning. That would have been more of a science-stopper than belief in the Bible, which states the universe had a beginning. Astrophysics caught up with the Bible and now we are witnessing the same phenomenon on the level of molecular biology.

[1] Francis Crick, quoted by Daniel James Devine, “Debunking Junk”, World magazine, 6 Oct 2012.
[2] Brendan Maher, “ENCODE: The human encyclopaedia”, Nature, Vol. 489, Issue 7414, 5 Sept 2012.
[3] NIH/National Human Genome Research Institute. “First holistic view of how human genome actually works: ENCODE study produces massive data set.” ScienceDaily, 5 Sep. 2012, Web 28 Dec. 2012.
[4] Stephen S. Hall, “Hidden Treasures in Junk DNA”, Scientific American, 8 Sept 2012.
[5] Fazale Rana, “Gene deserts take the life out of evolution’s best argument”, Reasons to Believe, 6 Apr 2011.
[6] Stephen C. Meyer, quoted by Daniel James Devine, “Debunking Junk”, World magazine, 6 Oct 2012.
[7] Tihomir Dimitrov, “50 Nobel Laureates and Other Great Scientists Who Believe in God, 2007.
Daniel James Devine, “Debunking Junk”, World magazine, 6 Oct 2012.

Wednesday, October 3, 2012

Why the papyrus fragment does not prove Jesus had a wife

The papyrus contains four words, written in Coptic, an ancient language used by Egyptian Christians. These translate into English as: “Jesus said to them ‘my wife’”. The words are written on a fragment about three inches by one and a half inches that was provided by a private collector. Karen King, Hollis Professor of Divinity at Harvard Divinity School, was given the fragment to analyze and translate. She reported the news of the discovery to the 10th International Congress of Coptic Studies.[1] The piece of papyrus is now in the hands of a private collector and nothing is known about the circumstances of its discovery.

If authentic, this papyrus appears to provide some interesting insights into cultural mores of the time. However, there are a number of reasons why it does not prove Jesus Christ was married. First, researchers have little or no context for the message on the fragment. Only a few lines of writing are partially able to be translated. Because there is writing on both sides, it appears to have been part of a book or codex, though at this time, none of the remainder of the codex has been made public, if any more even exists. Other writing on this fragment seems to reference an alleged discussion between Jesus and his disciples in which Jesus twice mentions his mother. It is speculated that an original may have been written in Greek, then translated into Coptic for Egyptian Christians. This is of extremely little evidentiary value on which to base any conclusion. We have no idea from where this fragment came or what was written in the rest of the codex.

Second, even if the fragment is authentic, it is dated to the late second century, about 150 years after the death of Jesus. Initial examination by experts seems to indicate the fragment is probably from this time period, based on the appearance, language and grammar, though additional chemical composition of the ink remains to be completed. In the second century and later, many pseudopigraphal “gospels” were written, such as the Gospel of Peter, Gospel of Thomas, Gospel of Mary and the Gospel of Judas. None of these were written by the named authors and none were written during the lifetimes of the apostles. These are typical of the Gnostic genre that was prevalent during that time period which were inferior to and frequently contradicted the authentic gospel accounts. The authentic gospel narratives (Matthew, Mark, Luke) were written during the middle of the 1st century or late 1st century in the case of John. These four were accepted by members of the church, many of whom had personally seen Jesus or the apostles and could attest to the narratives.

Dr. Simon Gathercole, Senior Lecturer in New Testament Studies at the University of Cambridge and expert on apocryphal gospels, commented on the fragment. He noted that, in relation to other gospel accounts, the language in the fragment most closely resembles some of that found in the Gospel of Thomas, a pseudopigraphal Gnostic writing. Here are a couple of the comparisons.

Thomas 101:3: My true Mother has given me life.
Fragment line 1: My mother has given me [life].

Thomas 114:1: Simon Peter said to them, “Let Mary come out from us, because women are not worthy of life.”
Fragment line 3: Mary is worthy of it. [2]

Third, reliable writings from the first century, which followed very soon after the life of Jesus, provide numerous details of his life, with no mention of a wife. These include the canonical gospels (Matthew, Mark and Luke) as well as writings of Peter, James and John, who had lived with Jesus. Furthermore, Paul’s 13 letters are well-authenticated to have been written prior to his death by A.D. 64 and these mention nothing of Jesus being married. In fact, Paul specifically mentions wives of the apostles when writing to the Corinthians around A.D. 54:
“Do we not have a right to take along a believing wife, even as the rest of the apostles and the brothers of the Lord and Cephas?” (1 Cor. 9:5)
If the apostles, such as Peter (Cephas) were cited as examples of those with wives, would it not have been significantly more impactful to mention the Lord’s wife, if he had one? And, it would seem to be contrary to Jesus’ character to marry when he knew he would be dying and returning to the Father at an early age, leaving behind a young widow.

Fourth, even the scholar who found the artifact cautions that it has not been verified as authentic. When asked if she has doubts regarding the authenticity of the fragment, Karen King told Time magazine: “Oh, yes, absolutely. I think something like this needs to be questioned further. “ [3]

Even liberal New Testament scholar John Dominic Crossan, who doubts the resurrection, has no doubts about Jesus being single. Using an avian analogy, he stated: “There is no evidence that Jesus was married (looks like a duck), multiple indications that he was not (walks like a duck), and no early texts suggesting wife or children (quacks like a duck), … so he must be an incognito bridegroom (camel in disguise).” [4]

Finally, regarding the fragment in question, Dr. Karen King wrote:
“It does not, however, provide evidence that the historical Jesus was married, given the late date of the fragment and the probable date of original composition only in the second half of the second century.” [5]

[1] Harvard Divinity School, “Jesus’s wife? Scholar announces existence of anew early Christian gospel from Egypt.” ScienceDaily, 18 Sept 2012. Web. 25 Sep. 2012.
[2] Simon Gathercole, “Did Jesus have a wife?” Tyndale House Residential Centre for Biblical Research, accessed 30 Sept 2012.
[3] Stephan Faris, “An Interview with the Discoverer of ‘Jesus’ Wife’”, Time World, 25 Sept 2012.
[4] Darrell L. Bock, Breaking the DaVinci Code, (Nashville, TN: Nelson Books, 2004), 31-32.
[5] Karen L. King, “Jesus said to them, ‘My wife…’” A New Coptic Gospel Papyrus, Forthcoming Harvard Theological Review 106:1, January 2013, p. 1.

Wednesday, September 12, 2012

Muslim lawyer in Iran is a hero

At great personal risk and facing a possible nine year prison term, Mohammad Ali Dadkha, a Muslim lawyer in Iran argued in court for the release of Christian Pastor Youcef Nadarkhani. On Saturday, September 8, the Christian Pastor was released after spending three years in prison for attempting to register a Christian house church and questioning the compulsory Islamic education of his children. In 2010, the pastor was sentenced to death and Iran’s judiciary upheld the sentence in February. [1]

We commend the courageous actions by Dadkha for advancing religious freedom in a society that is not especially tolerant of Christians (or other faiths). The lawyer has previously defended 11 Christians in Anzaly and eight in Shiraz who were arrested for their religious activity. He is one of the few human rights lawyers in Iran who has not yet been imprisoned. Dadkha co-founded Iran's now-banned Center for the Defense of Human Rights along with Nobel Peace Prize laureate Shirin Ebadi. The Christian Post reported that, last month, the lawyer was informed he would be receiving a nine-year sentence for "acting against the national security, spreading propaganda against the regime and keeping banned books at home." [2]

In May 2012, it was reported that Dadkha was under immense pressure to make false television confessions. “Tomorrow is my last day to either make television confessions or go to prison. I will go to prison, and I will not [be forced to] leave my homeland,” he said. “They told me that if I didn’t confess, they would enforce my sentence. They talked to me for long periods of time and I did not accept it. I will say now that if one day I say things, they are not credible and I must have been under conditions where I was forced to say those things. I hope God maintains my power.” [3] We are thankful for Dadkha and hope others will be as courageous as this man for the right of religious freedom.

[1] Benjamin Weinthal, Jerusalem Post, “Iran releases persecuted Christian Pastor”, 8 Sept. 2012.
[2] Katherine Weber, Christian Post, “Youcef Nadarkhani Is Free, But His Lawyer Still Faces Threat of Imprisonment”, 11 Sept. 2012.
[3] International Campaign for Human Rights in Iran, “’Confess on TV or Go to Prison,’ Authorities Tell Dadkhah” 14 May 2012.

Friday, September 7, 2012

Bible burning and blasphemy?

Have you heard about the group of angry Christians gathered around the house of a 14-year old Muslim girl with Down’s syndrome, threatening to kill her, burn her house and the houses of other Muslims in the area? And, that this occurred after a neighbor reported the girl was seen burning pages of the Bible. In this region where Christians are in the majority, hundreds of Muslims have fled their homes in fear. About 300 Muslims set up a camp outside of the city, from where they were later ejected and the make-shift mosque they had constructed was burned.

Has anyone seen this story in the news? Of course not, because none of the above happened. Well, not exactly. The story is accurate if we switch the Muslim and Christian references. The truth is that Rimsha Masih, the 14-year old girl with Down’s syndrome was jailed in Islamabad, Pakistan and hundreds of Christians fled their homes in fear. Under Pakistan’s blasphemy law, the girl faces a possible death sentence if found guilty of insulting Islam or the Quran. [1] Christians who fled are without food in many cases, except for some assistance provided by relief organizations. Zahid Pervez, whose house has been looted of its few valuable possessions, said "We'll never go back. We have young children. How can we go back? They won't even let us say our prayers there." A neighbor reported that the girl and her mother were beaten by a mob that formed outside their house.

And yet, in the USA, Christians are labeled as intolerant, bigoted and hateful. In Pakistan, a council of Muslim clerics and scholars, to their credit, joined hands with the Pakistan Interfaith League - which includes Christians, Sikhs and other religions - to call for justice for the girl. [2]

Sunday, in a plot twist, a Muslim cleric was arrested and charged with planting pages of the Quran in the girl’s shopping bag. Her lawyer plans to request a dismissal of the charges, though he still agrees the blasphemy law is a good law. Today, the girl was granted bail – one million rupees, about $10,500 - which was paid by a humanitarian organization. However, she’s not out of the woods yet, as people accused of blasphemy who are not convicted often face vigilante justice. A Pakistani man in this situation in July was dragged from a police station and beaten to death before his body was set on fire. And, two politicians who criticized the blasphemy law were murdered last year. [3]

What is the difference between this response to insult and that which is advocated in the Bible by Jesus and His apostles? Jesus instructed us to “love your enemies and pray for those who persecute you” (Matthew 5:44). The Apostle Paul stated: “when we are reviled, we bless” (1 Cor. 4:9) and “see that no one repays another with evil for evil” (1 Thess. 5:15). The Bible informs us that those who know God have love for others and “the one who does not love does not know God, for God is love” (1 John 4:8). The Bible instructs believers in Jesus to live in peace with others (Matt. 5:9, Rom. 12:18, 1 Cor. 7:15).

When Bibles are burned, angry mobs of violent Christians do not form, nor should they. All religious beliefs must be tolerated as long as the adherents do not harm others. As followers of Jesus, we denounce any violence or oppression in the name of religion and call for freedom to openly discuss issues of faith, without fear of retribution. Let’s have a civil discussion in an atmosphere of mutual respect. Christians do not hate those who persecute our brothers and sisters; rather, we love and pray for them. Religious beliefs must not be coerced by force, but demonstrated through love and open dialogue.

[1] The NY Daily News India, “Father of Pakistani Christian girl appeals to President Asif Ali Zardari”, 28 Aug 2012.
[2] Saeed Shah in Islamabad, The Guardian, “Pakistani Muslim leaders support Christian girl accused of blasphemy,” 27 Aug 2012.
[3] Taha Siddiqui, Christian Science Monitor, “As Pakistani Christian girl is granted bail, critics call for blasphemy law reform”, 7 Sept 2012.

Sunday, July 22, 2012

Belief in God leads to brain damage

Yes, that is an actual conclusion of a scientific study conducted at the Center for the Study of Aging and Human Development, Duke University Medical Center, Durham, North Carolina. Researchers Amy D. Owen, et. al., studied neuroimaging data from MRI measurements to assess the relationship between religious factors and structural neuroanatomy, specifically hippocampus volume in the brain. The hippocampus has been associated with memory consolidation, learning and influencing of emotions via connections with the amygdala. Atrophy of this brain structure later in life has been associated with dementia, Alzheimer’s disease, depression and lessened ability to form new memories. The study found that people who reported having a life-changing religious experience showed increased hippocampal atrophy from base line to final assessment among born-again Protestants, Catholics, and those with no religious affiliation.

Participants in the study, conducted between 1994 and 2005, were 268 men and women over the age of 58. Religious factors assessed included frequency of public worship, private activity (prayer, meditation, or Bible study), and religious group membership. Baseline and annual factors assessed included born-again status and life-changing religious experiences. The study found that those who reported a born-again or life-changing religious experience suffered greater hippocampal atrophy during later life. The authors interpreted the findings by hypothesizing that cumulative stress, producing glucocorticoids, led to decreased hippocampus volume.

Some covariates that may impact the results were studied, including social support, self-reported stress and depression. These and other variables require more research in connection with the results found. It is questionable whether this study adequately considered other factors, such as prescription drug use, diet, exercise, non-religious life stressors, mental activity level, and so on. And, is it possible the causal relationship is reversed? Perhaps the self-perceived effects of aging may lead one to sense his or her own mortality, leading one to more diligently seek a religious experience. Causal relationships between brain anatomy and emotional/psychological factors are always tenable at best.

The study speculated that stress may be present for born-again Christians as a result of being a religious minority. However, that conclusion seems unfounded because most of the demographic sample included Southeastern Protestant Christians, hardly an oppressed minority in that part of the USA. The researchers' primary premise seems accurate (though not the secondary conclusion), that stress-induced cortisol in the body can affect the hippocampus, and is supported by other research. In particular, returning Gulf War veterans suffering from chronic PTSD exhibited smaller hippocampal brain regions in MRI exams than a control group. An additional interesting finding is that therapeutic treatment seems to be associated with an increased hippocampal volume after six months, indicating a resilience.[2] Perhaps born again Christians can be treated? The secondary conclusion, that people with a life-changing religious experience suffer more stress, seems irrational, particularly in light of other studies that indicate positive emotional and psychological benefits of religious experiences.

A few points need to be made here. First, if the hypothesis of the researchers is accurate – that increased stress leads to increased glucocorticoids, thereby damaging the hippocampus – would it not seem reasonable that people who have had a life-changing religious experience would experience less stress? Almost by definition, an experience that is life changing would seem to bring more peace and contentment to one’s life. How would a life-changing religious experience lead to more stress? The researchers own hypothesis seems to be contradicted by the results of the study.

Second, since millions – perhaps billions – of people throughout history, across all cultures, claim to have strong religious beliefs, does this study conclude they were also brain-damaged? It is a well-known fact that many people from all races and geographical locations through all of recorded human history have believed in some deity, afterlife, and/or spiritual experience. Not all of these are of the evangelical Christian variety. The bias of this study is striking – the group studied were Christians, not Hindus, Muslims, or Rastafarians. The control group – those supposedly with normal cognitive anatomy – were those with no religious affiliation.

Third, other studies have found there is not necessarily the supposed direct connection with hippocampal size and mental function, such as memory. In the December 22, 2011 issue in the journal Neuron, Dr. Jordan Poppenk, Baycrest's Rotman Research Institute, found some evidence that extensive spatial memory acquisition leads to enlargement of the posterior hippocampus and a decrease in the anterior hippocampus. In other words, there may not be a direct one-to-one relationship between size and memory capabilities. Poppenk stated, "This suggested to us that the crucial predictor of individual differences in recollection ability might not be the overall size of the hippocampus but the separate contributions of the posterior and anterior segments of the hippocampus." [3]

In conclusion, much evidence links religious and spiritual involvement with improved mental health. [4] And, a study conducted of more than 20,000 adults representative of the U. S. population found that an average life expectancy difference of seven years for those who attend church or religious services over those who do not. [5] Perhaps, during those seven years, they were brain damaged as well.


[1] Owen AD, Hayward RD, Koenig HG, Steffens DC, Payne ME (2011) Religious Factors and Hippocampal Atrophy in Late Life. PLoS ONE 6(3): e17006.doi:10.1371/journal.pone.0017006.
[2] Brigitte A. Apfel, Jessica Ross, Jennifer Hlavin, Dieter J. Meyerhoff, Thomas J. Metzler, Charles R. Marmar, Michael W. Weiner, Norbert Schuff, Thomas C. Neylan.Hippocampal Volume Differences in Gulf War Veterans with Current Versus Lifetime Posttraumatic Stress Disorder Symptoms. Biological Psychiatry, 2011; 69 (6): 541 DOI: 10.1016/j.biopsych.2010.09.044
[3] Cell Press, “Gauging individual human memory from scans of brain’s hippocampus?” ScienceDaily, 20 Jan 2012, Web 22 Jul 2012.
[4] Raymond F. Paloutzian, et. al., Handbook Of The Psychology Of Religion And Spirituality, (New York, NY: The Guilford Press, 2005), 446.
[5] Robert A. Hummer, et. al., “Factors Affecting Mortality”, Demography, Volume 36, Number 2 (1999), 273-285, DOI: 10.2307/2648114.

Sunday, July 1, 2012

IAG-BB3, Pool of Siloam

(Information about God – Brief Byte 3)
Historical accuracy of the Bible is unparalleled among major world religions. One example involves the Apostle John’s report that Jesus put clay on the eyes of a blind man and told him to wash in the pool of Siloam. When the man did, he was healed and could see (John 9:1-6). The pool is also mentioned in Nehemiah 3:15 and Isaiah 8:6, referred to as the “Pool of Shelah”. In 2004, conclusive evidence for the pool was discovered by archaeologists Eli Shukrun and Ronny Reich during excavation for a drainage pipe. Several steps were also discovered, perhaps the same ones used by the blind man. The pool was fed by the Gihon Spring. Archaeologists found coins that dated from the biblical era with ancient Jewish writing, with pottery shards and a stone bottle cork, all of which helped to confirm this is the location of the Siloam Pool, according to a report by MSNBC. This discovery, while not proving the healing by Jesus, does provide another in a long list of discoveries which confirm the historical accuracy of the Bible.

Sunday, June 24, 2012

IAG-BB2, Intelligence produces information

IAG-BB2
Information about God – Brief Byte 2
(Everyone’s busy, so this is very short, but informational.)

Critics charge that Christians employ a “God of the gaps” rational to account for biological systems that are not yet explained. Invoking an intelligent designer when an evolutionary process has not yet been discovered is labeled as anti-scientific. But that’s not true, particularly regarding information in the cell. The complex specified information encoded in the DNA of every cell can be explained. All causal information of this type is produced by an intelligent mind. This includes words in a book, radio signals, hieroglyphics and computer programming language. The data encoded in DNA is not only highly complex, comprised of three billion base pairs (in humans), but is also purposeful. The DNA molecule contains the blueprint design specifications for all of the biological systems in an organism. “Whenever we find specified information and we know the causal story of how that information arose, we always find that it arose from an intelligent source. It follows that the best, most causally adequate explanation for the origin of the specified, digitally encoded information in DNA is that it too had an intelligent source” (Stephen C. Meyer, Signature in the Cell, p. 347).