Thinking to Believe

The chimp Y chromosome has now been fully sequenced, and the results are astounding.  A study in Nature reveals that the chimp Y chromosome is radically different than the human Y chromosome.^[1]  The chimp’s Y chromosome has only two-thirds the number of distinct genes/gene families, and 47% of the protein coding regions compared to its human counterpart.  Furthermore, more than 30% of the entire chimp Y chromosome has no counterpart in humans.  Even those segments that do have counterparts in the human Y chromosome are often located in different regions of the chromosome. 

One the lead researchers, David Page, told Nature News that “it looks like there’s been a dramatic renovation or reinvention of the Y chromosome in the chimpanzee and human lineages.”^[2]  Of course, this reinvention has to be explained in terms of common descent, so they speculate that the chimp Y chromosome experienced a loss of DNA, while humans experienced a gain.  The surprise of the scientists involved, however, demonstrates that this find is counter-intuitive to Darwinian expectations.

HT: Evolution News & Views

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[1]Jennifer F. Hughes, David Page, et al, “Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content”; Nature 463, 536-539 (28 January 2010) | doi:10.1038/nature08700; Received 3 August 2009; Accepted 24 November 2009; Published online 13 January 2010; available from http://www.nature.com/nature/journal/v463/n7280/full/nature08700.html; Internet; accessed 30 April 2010.
[2]Lizzie Buchen, “The Fickle Y Chromosome”; available from http://www.nature.com/news/2010/100113/full/463149a.html; Internet; accessed 30 April 2010/

I have little confidence in the United Nations.  In my opinion, it is a spineless political organization.  Giving Iran a seat on the human rights body, “Commission on the Status of Women,” however, lets me know that the UN is corrupted beyond repair.  If Hitler was alive today, surely he would be given a chair on a committee for Jewish rights.  Unbelievable.

Hawaii’s Senate approved a bill providing civil unions to same-sex and opposite-sex couples in January 2010.  Yesterday, their House of Representatives approved it as well.  It remains to be seen whether the governor will veto it.

Franklin Graham was invited to the Pentagon to offer a prayer on May 6 for the National Day of Prayer.  The Military Religious Freedom Foundation (of all entities) is objecting to Graham’s invitation because he has called Islam an “evil” religion, and they say his presence will offend Muslim soldiers.  So now the Army is considering rescinding the invitation.  Maybe I failed to get the memo, but the last I checked part of religious freedom is the freedom to think one’s own religion is true, and all others are false (and perhaps even evil).  

This is what religious pluralism gets you: censorship of anyone who thinks their faith is actually true, and is willing to spell out the logical corollary to this belief, namely, that other religions must be false.  That religious view will not be tolerated by the preachers of religious tolerance.

In Isaiah 55:8-9 we read the word of YHWH: “For my thoughts are not your thoughts, neither are your ways my ways, declares the LORD. 9 For as the heavens are higher than the earth, so are my ways higher than your ways and my thoughts than your thoughts.”

In my experience, this Scripture is usually quoted in two contexts: (1) when we are ignorant of some knowledge; (2) when our position is being decimated by our opponent’s evidence, and we lack a sufficient response.  Neither use is legitimate because both are taking the passage out of its context.  

Verse 7 reads, “Let the wicked forsake his way, and the unrighteous man his thoughts; let him return to the LORD, that he may have compassion on him, and to our God, for he will abundantly pardon.”  The Lord’s way/thoughts are contrasted to the ways/thoughts of the wicked, not the righteous.  The Lord’s point is that His ways/thoughts are superior to the ways/thought of the wicked, not that His ways/thoughts are incomprehensible to mankind in general.  That’s not to say we can fully understand God and His ways, but it is to say that this passage is not teaching divine incomprehensibility, but rather divine superiority.

(Note: Read Part 3a of the series before reading this post)

Viruses

The HIV virus mutates at the evolutionary speed limit: 10,000 times faster than most cells such as malaria.[1] And its genome is rather small (nine genes versus thousands in malaria).[2] Its small size combined with a short generation time (1-2 days) and super-rapid mutation rate means every single nucleotide in the HIV genome will mutate 10,000 to 100,000 times in every infected person every day, and thus double point mutations like the one that made malaria immune to Chloroquine occur in every person every day.  In fact, over the past several decades every possible combination of up to six point mutations has occurred in HIV somewhere in the world.  If RM drives macroevolutionary changes in organisms, then we should observe macroevolution in the HIV virus since it experiences more mutations than any other organism.  But we don’t.  HIV has run the gamut of all possible mutations to its genome, and yet with all of these mutations in a population of 100 billion billion viruses, no new cellular machinery has been created, and no new organism has developed! HIV is still HIV.  It still contains the same number of proteins, still performs the same function, and still binds to its host the same way it always has.  There have been no significant biochemical changes.  Even gene duplication has failed to produce any new biological information.

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George Washington and Abraham Lincoln must be rolling over in their grave.  A U.S. District judge in Wisconsin has declared that national days of prayer are unconstitutional because they violate the separation of church and state.  

Those like this judge are very confused about the first amendment.  What was intended to grant the freedom of religion is being used to guarantee a freedom from religion.  The 1^st amendment did not demand that the government be purely secular with no mention of, or interaction with religion.  Washington and Lincoln et al proclaimed national days of prayer and fasting, and no one ever thought of these acts as being unconstitutional.  In fact, for more than 200 years no one thought so.  The text hasn’t changed, so how did we discover something that those who penned and ratified the amendment didn’t know about?  

These kinds of rulings are clearly not based on the text of the Constitution, because the Constitution does not prohibit religious expression, even by the government as the government.  It only prohibits Congress from passing a law establishing a particular religion as the nation’s religion.  It does not proscribe government officials from speaking about religion, or establishing a day of prayer.  After all, no religion is established as our nation’s religion by proclaiming a national day of prayer.  Prayer is common to many religions.  This ruling is based on the secularist philosophy of the day, not the Constitution.

President Obama has instructed the Health and Human Services Department to draft rules that grant patients the right to designate who can visit them in the hospital.  Not only would this open the door for non-relatives to visit their loved ones in the hospital, but also gay partners.  I support this law for several reasons.  First, I have always found it ridiculous that hospitals, not patients, determine who can visit the patient.  Secondly, this will remove one of the standard arguments for same-sex marriage (SSM).  Many proponents of SSM argue that SSM is necessary to give them the right to visit their partners when hospitalized.  Apparently, SSM isn’t needed for that after all.  Like so many other practicalities, these privileges can be ascertained via other legal means wholly apart from marriage.

(Read parts 1 and 2 in the series)

The heart of the neo-Darwinian synthesis is that evolution advances via the process of natural selection working on random mutations (RM+NS).  Natural selection itself lacks any creative power – it only eliminates what doesn’t work.  Eliminating the unfit, however, does nothing to “explain the origin of the fit”![1]  The burden falls entirely on RM to create the biological novelties required by Darwinism to drive evolution forward.  It must be asked, then, whether RM has the creative power required by Darwin’s theory.  Can RM produce the new biological information necessary to drive evolution forward and explain the diversification of all life?  What exactly can RM do? 

When the neo-Darwinian synthesis was set forth some 70 years ago, answers to these questions could not be ascertained.  While the theory was plausible on a conceptual level, there was no real way of testing its biological plausibility.  Over the last 30 years, however, we have been able to observe both the power and limits of RM+NS at the biological level.  What have we discovered?  We discovered that while RM can produce variability within an organism, it is not capable of producing the kind of changes required by Darwin’s theory.  RM is severely limited in what it can accomplish. 

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Nebraska passed and signed a bill into law Tuesday April 13 that prohibits abortion after 20 weeks on the basis that fetuses at that stage of development can feel pain.  This law directly challenges the Supreme Court’s 1992 Casey decision, in which they said a state cannot place an undue burden on a woman’s right to an abortion prior to the point of viability, which is currently ~22-24 weeks.  This law, then, directly challenges the Supreme Court’s ruling, offering an alternative basis for prohibiting abortion, and which results in more restrictions against abortion.  The law will surely be challenged.  If it goes all the way to the Supreme Court, Nebraska will have to persuade the court that fetuses can feel pain at 20 weeks, and that the ability to feel pain should be the standard by which an “undue burden” is judged.  We’ll have to wait and see what happens.

A 34 year old anonymous journalist writes about her abortion experience in Salon.  Her description, like so many others’, makes it clear just how emotionally damaging abortion is for women.  Can you think of any other medical procedure that causes someone so much emotional pain?  I don’t know anyone who agonizes and weeps over the decision to remove their tonsils.  The sort of response described by the author cannot be explained in terms of prior moral sentiments against abortion because the author is clearly pro-choice, and expresses no regret for having an abortion.  Shouldn’t it be obvious that abortion is immoral when even those who think it is morally benign cannot convince their emotions that this is true?  

This is a painful, but good read (despite the very political ending which seems quite out of place and irrelevant).

HT: Jivin Jehoshaphat

(For part 1 in the series, click here)

If macroevolution occurs, it must do so at the biochemical level.  Additional genetic information is needed to build the new proteins and biological systems required for large-scale changes.  Where does the new biological information come from?  Mutations?  No.  Point mutations such as inserting, inverting, or substituting nucleotides in existing genes cannot increase the information content of DNA even if they occur in protein-coding regions, and even if the mutations are beneficial to the organism.  At best they can only replace existing information/function with different information/function, so that the overall information content is merely preserved.[1]  For macroevolution to occur a net increase of information is required, not just a change in existing information.

The origination of new genetic information requires new proteins, which requires hundreds of additional nucleotides arranged in a highly specified order.  How likely is it that chance processes can get the job done?  Next to none.  The chances of producing a functional amino acid sequence of a mere 150 nucleotide bases (which would sequence one of the smallest proteins) is 1:10¹⁶⁷.[2]  To put this number in perspective, consider that there have only been 10¹³⁹ events in the entire universe since the Big Bang.[3]  So even if every event in the history of the universe was devoted to building a single functional protein, the number of sequences produced thus far would be less than 1 out of a trillion trillion of the total number of events needed to give it even a 50% chance of success!  Any reasonable person must conclude, then, that it is beyond the reach of chance to create even the smallest amount of new biological information in an organism.  Add to this the fact that many new proteins are needed to produce new biological systems, and the scenario becomes all the more fantastical.  If chance alone cannot produce the gene for even one protein—yet alone many—macroevolution becomes impossible.

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In recent days I have taken up a task I had given up on a number of years ago: harmonizing the resurrection accounts in the Gospels.  I hope to blog on this in considerable detail in the future, but wanted to explore a particular anomaly I have encountered that has me befuddled – an anomaly I am hoping you, the community, can help me resolve.

All of the Evangelists – with the exception of Luke[1] – report that Jesus appeared to several of Jesus’ women followers after they saw the angels in the empty tomb, but before they reported the incident to the apostles.  Luke, however, does not mention a resurrection appearance to the women.  According to Luke the women discover the empty tomb, encounter angels who tell them Jesus is risen, and then leave to tell the disciples what they had seen and heard.[2]  If this was all there was to Luke’s account it would not be much of a problem, since each of the Evangelists omit certain details that the others chose to include.  While it would be a curious detail to omit, its omission would be just that: a curiosity.

But the story is complicated by the testimony of the two disciples on the road to Emmaus.  

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Several months ago I blogged my way through Stephen Meyer’s Signature in the Cell, summarizing his devastating critique of naturalistic origin-of-life theories and powerful argument for the intelligent design of the first life (parts 1, 2, 3, 4, 5, 6, 7a, 7b).  But what about the proliferation of life?  Can a fully naturalistic theory like neo-Darwinian evolution account for the proliferation and variety of life once it began?  To answer this question I am going to summarize Michael Behe’s key argument against a Darwinian account of evolution in The Edge of Evolution (paperback only $6 through Amazon right now, regular $15). 

What Needs to be Explained

To properly evaluate Darwin’s theory of the evolution of life, we must clarify what is meant by “evolution.”  Evolution can refer merely to small biological changes within a species over time.  Called “microevolution,” or the special theory of evolution, this definition of evolution is relatively uncontroversial and has been confirmed empirically (e.g. drug resistance in bacteria, changes in the size of finch beaks, etc.).  Evolution can also refer to large-scale biological changes[1] that, over time, transform one species into another into another ad infinitum.  This kind of evolution is called macroevolution, or the general theory of evolution.  Darwin’s theory entails this latter definition, and thus proof for his theory requires evidence that there are no natural limits to the amount of variation an organism can experience.

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John Hoopes of the University of Kansas claims to be a scientist, but it is clear to me that he’s no scientist!  How do I know?  Because he has concluded that some intelligent designer is responsible for producing 300 of these:

Surely he knows scientists cannot appeal to intelligent agency as an explanation for natural phenomenon.  Besides, there is no need to appeal to any intelligent designer.  Natural processes such as wind and water erosion are fully capable of producing the spherical shape of these rocks over billions of years.  To appeal to some “rock-designer-of-the-gaps” is to give up on science.  Currently, we may not know the exact pathway by which nature produced these spherical rocks, but given the past successes of science, I am sure we will discover it in the near future.  

If these rocks are the products of some intelligent designer as Hoopes claims, then let him tell us who designed the designer.  Guess what, he doesn’t know!  Clearly, then, these rocks can’t be designed.

A few weeks ago the famed atheist and philosopher of science, Michael Ruse, wrote a response in the Guardian to the question, What can Darwin teach us about morality?  Ruse’s multifaceted answer is accurate, intriguing, and at times, incoherent – but always and thoroughly enlightening about where atheistic and evolutionary thought leads. 

Ruse admits that without God “there are no grounds whatsoever for being good.”  Morality, he says, is just a matter of emotion and personal taste on the same level as “liking ice cream and sex and hating toothache and marking student papers.”  But he’s quick to point out that just because there are no grounds for being good, it doesn’t mean we should be bad.  While this is true insofar as it goes, it fails to answer the more important question: Why – in the absence of a moral law giver, and thus in the absence of any objective moral law – should anyone behave in ways traditionally thought to be “good” if and when it is in their own self-interest to do otherwise?  In the name of what should they deny their own impulses?  In the name of the Grand Sez Who?

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