Creationists and IDists v. BioLogos

This post is a little complicated, but it is important concerning the "evolution wars," and I've edited a few times to make it as clear as I can. To start, BioLogos is a group of people who are committed to "Theistic Evolution" (TE). TE is the premise that animals and humans developed by evolution helped along by God. Theoretically this help could come directly, such as if He intervened in the genes of an embryo to be therefore born slightly different than its parents. This approach does have the problem of people coming from animals. Or, in the version pushed by BioLogos, God could have acted in a Divine Hands-off manner (also known as Deism). This scenario supposes that God somehow caused evolution to happen in a pre-planned way that would LOOK to us as random.

There are several problems with this Deism view. One problem is that on a physical level it correlates exactly with any secular or atheist’s view of evolution, what we call neo-Darwinian evolution. Secularists look at evolution as random (the random genetic mutation element means the basis of evolution is random even though there is a non-random element called selection). Another problem with this view is that there is a logical fallacy in saying life LOOKS LIKE it was brought about in a random way because biological structures do NOT LOOK random. Our bodies have trillions of cells working together to give us life. A cell is a basic unit of biology. Proteins, which are the working molecules of the cell, are very specifically constructed for what they do. The DNA inside the cell acts as a code to make the proteins, and therefore must also be very specific. These molecules do not look random.

So we have a group of people (BioLogos), many of whom are scientists, who tell us God somehow created animals and plants and people, but we are supposed to go by the book of all secularist and atheist scientists. In contrast there are other groups of people who are actively questioning the secular view and secular-like TE view put forth by BioLogos. One group of Intelligent Design (ID) advocates is called the Discovery Institute. These people are dedicated, among other things, to make the facts known about proteins and other biological structures and claim these structures were designed. They are using scientific methods, such as information theory, to try to prove what they are saying. Other groups are Special Creationists (believing in direct supernatural creation by God), such as Answers in Genesis and the Institute for Creation Research. These also have scientists in their ranks and are using their websites to argue their cases.

Since BioLogos backs atheistic outlooks on creation and evolution, the arguments of the Discovery Institute and Creationists are directed against both Biologos and atheists. On the Discovery Institute’s newsletter website and his own, Darwin's God, Dr. Cornelius Hunter is showing why the BioLogos arguments are wrong. A very good example is in the post "Shared Errors: BioLogos on broken genes," Darwin's God (May 31, 2016).

So a major problem with BioLogos is though they say they want to show how science and religion can be reconciled, they promote both a non-religious and non-scientific (illogical) view of evolution. They imply that God is not really needed because evolution is random anyway, and that if you want to believe in God, you still better believe in non-divine-type evolution.

The person who started BioLogos, Dr. Francis Collins, a self-professed Christian, has been instrumental in the present legal status of using human embryos in scientific research. Though the BioLogos people profess to be Christian, neo-Darwinian evolution has been the only option until recently for atheists (for a new alternative, see The Third Way of Evolution).

Casey Luskin, who worked for Discovery Institute for many years, has published a paper about the relationship between atheism and the teaching of evolution. It is Casey Luskin, "Darwin's Poisoned Tree," Trinity Law Review 21, 1 (Fall 2015): 130-233. You can find the paper description and link to a PDF file at the link in the title.

It is not unusual for Christians to be right about some things and wrong about others. This is part of growth and learning. BioLogos Christians are wrong to push their random evolution agenda. Somehow they are blinded, perhaps by some imagined promise of scientific discovery, to the amazing design in biology that is obviously seen by others as supernatural creation. Refer to the Bible in resisting intimidation by scientists who tell you we came about by chance:

Ever since the creation of the world, his invisible attributes of eternal power and divinity have been able to be understood and perceived in what he has made. As a result, they have no excuse (Romans 1:20 NABRE).

Deaconess

The Pope made world-wide news Thursday by announcing he would set up a commission to study women deacons in the Catholic Church. What a historic move! His decision came about after an international meeting with consecrated women and International Union of Superiors General. An article about the circumstances is HERE at the Crux website.

The women had written questions for the Pope (4 main topics) which more or less asked why women still do not have a say in the Church and why we are barred from being deacons. The questions can be read HERE.

I am excited for a few reasons. I have said before that women should be deacons. They should be ordained as deacons. Married men are ordained as permanent deacons, and if the Church leadership insists on only male priests, women can at least be permanent deacons. It is just not right for the Church to have seven sacraments for men and six for women. Another reason they should be named deacons is that many do the work of deacons anyway. But men can be ordained and women not. It is just plain discrimination. I know many will say there are reasons to keep women out, but there were rationalizations to keep African-Americans out of seminaries at one time. We all know of the terrible prejudice against African-Americans in general, but not so much about how this carried over to Catholics (see the book by Cyprian Davis, The History of Black Catholics in the United States).

Of course, the question of who will be on the commission for women deacons is next. Obviously, if the members are all conservative bishops, women will not have a chance. The pope has been fairly astute about these things. He has been placing more progressive persons in critical roles. However, the current prefect of the Congregation for the Doctrine of the Faith at the time this post is first published, Gerhard Cardinal Muller, is conservative. Perhaps the Pope hides behind him a bit. After a previous commission’s look into the female diaconate, Muller made a statement along the lines that women will feel discriminated against if they are allowed to be deacons but not priests or bishops. Zenit reports this HERE.

Apparently the consecrated women who asked the Pope to become deaconesses do not have that problem. Nor do some others. A link to the organization called Catholic Women Deacons is HERE.

The Internet is buzzing, including the website I follow, Catholic Answers Forums (CAF). I think it is a topic that will not go away. We should all pray for discernment into what is best for the Church and especially for doing the Lord's will.

Smallest Cell

An interesting discovery from the J. Craig Venter Institute is reported by Rachel Feltman, "This man-made cell has the smallest genome ever — but a third of its genes are a mystery," Washington Post, March 25, 2016. The article describes the smallest cell genome to which the scientists were able to reduce, and it turns out it is twice as big as they thought it would be.

DNA is the molecule that forms our genes. These are used for coding proteins, which do the work of our cells. Cells are the basic unit of biology and its complete set of genes is the genome. DNA is also needed for reproduction, to pass the information to offspring.

Humans have trillions of cells, and most of them contain their own set of DNA. Some organisms, like bacteria, have only one cell, but still need DNA to make protein and for reproduction. As you have probably seen portrayed somewhere, DNA looks like a twisted ladder. Each step of the ladder has a smaller molecule that acts, in sequence with the other steps, as a code for the protein so it can be made correctly. There are 4 types of steps which are called bases and in bacteria it takes about 1000 bases per gene. And as the WP article points out, “to build a DNA code that will support life, you need to be pretty much error-free.” More information on DNA can be found at the CreationWiki entry HERE.

Scientists have been trying to determine what is the least number of genes a single cell, such as a bacterium, can have and still stay alive. This is not a fully-functional cell in the sense it would have to be given nutrients that it could not produce itself. Scientists had thought the number would be in the vicinity of 250, but have found, at least in this approach, that more genes are needed than they thought. They came up with 473 and were surprised they could not find the function of 32% of them. The organism needs over 531,000 base pairs in order for it to keep "working."

An abstract of the actual scientific paper is Hutchison III et al., "Design and synthesis of a minimal bacterial genome," Science 351, 6280 (March 25, 2016).

Eugene Koonin, the director of comparative genetics at NIH, estimated a fully functional cell would need about 1000 genes. These would be fully self-functional, not needing supplements fed to them. At 1000 bases per gene, that would be one million bases in exact order. The article which contains his estimate can be found here in Koonin, Wolf, "Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world," Nucleic Acids Research, 36, 21 (Dec. 1, 2008): 6688-6719.

What are the chances that even half of that, an exact sequence of 500,000 bases, could have randomly come together to start life, composing a complete genome which codes for life processes (even if there were nutrients in the environment) such as breakdown of sugar to make the structures of the proteins, reproduction and other functions, and organize all of it in tiny cells? This could not have happened by chance even in billions of years.

Praise God through Jesus Christ for His Creation.

Amoris Laetitia

I just finished reading Pope Francis’ Apostolic Exhortation on marriage and the family, Amoris Laetitia (March 19, 2016). It is translated, The Joy of Love, and is a culmination of two years of Vatican-sponsored meetings and input concerning the family. With the explosion of the number of divorces, there has been an increasing pressure from liberals (progressives) to change the Church’s response to those who have divorced and remarried. This is especially because these persons are not allowed to partake of the Eucharist in the mass. The divorced complained that a repentant murderer can receive communion while they can’t. On the conservative (traditionalist) side, marriage is held as a metaphor for Christ’s relationship to His church, and therefore indissoluble. One of my own interests in the document is from the viewpoint of how women are treated by the Church, and I was pleasantly surprised to see some understanding.

Pope Francis agrees to the Christ-Church-marriage comparison, but with the understanding that people are not as perfect as Christ and therefore their marriages will not be perfect. The pope continues to hold up a good marriage as a difficult but attainable goal, worthy of all its efforts. Yet he asks for the mercy of those who interact with married couples and for the divorced and re-married Catholics who feel ostracized by not being allowed communion. The pope maintains these people are not excommunicated and should not be made to feel as such. To conservatives who don’t want change, any thought of giving them communion is a liberal viewpoint that they fear will lead to a downhill slide of the entire institution of marriage.

I found some of the most refreshing sentences in the whole exhortation Amoris Laetitia to be in Sections 36 and 37. In 36, Pope Francis comments on the overbearing emphasis of Church leaders on procreation that made Catholicism seem more about having the maximum amount of children instead of focusing on the divinity of Jesus Christ. Of course having children is important, but I don't think every married person is called to parenthood. And unfortunately not all children come to believe in God. But we are all called to worship and evangelize the nations for Jesus Christ. Section 36 has this sentence:

Then too, we often present marriage in such a way that its unitive meaning, its call to grow in love and its ideal of mutual assistance are overshadowed by an almost exclusive insistence on the duty of procreation.

Then, speaking of clergy, in 37 Pope Francis wrote: 

We also find it hard to make room for the consciences of the faithful, who very often respond as best they can to the Gospel amid their limitations, and are ca­pable of carrying out their own discernment in complex situations. We have been called to form consciences, not to replace them.

How important this is in contrast to the effort to control people.

Another section I like is 54, which speaks of women’s rights. It says emancipation of women is not to be blamed for all the woes of marriage. The pope writes:

If certain forms of feminism have arisen which we must consider inadequate, we must nonetheless see in the women’s movement the working of the Spirit for a clearer recognition of the dignity and rights of women.

Thank goodness. Let us hope this is a dawn finally of a new worldview about women. I’m not saying women always will make the right decisions or discern correctly, but I believe we can be as capable as men of doing so.

It remains to be seen what will actually happen in response to the paper. The Germans have been chafing at the bit to make changes, as are progressive groups of priests in Ireland and the US. But the tensions persist because there are plenty of conservatives up in arms and writing about it. One article is by Raymond Cardinal Burke, "'Amoris Laetitia' and the constant teaching and practice of the Church," National Catholic Register, April 12, 2016, basically saying that bishops and priests don’t really have to follow it. Conservative bloggers are complaining as well.

Pope Francis, though he says he encourages dialogue, has in turn had some pretty harsh words for conservatives: Carol Glatz, "'Witch hunts' rooted in putting laws above God's truth, pope says,"  Catholic News Service, April 11, 2016. The tensions are simmering and though it is rather fascinating to watch, it is not good for the Church to be mired in disagreements. When Catholics, leaders or lay, are so diverse, we need to pray for discernment. I’ve found, though, that persons can be so tied to one worldview, they can’t imagine any other having merits. This is a block to listening to other people.

However, what happens when different people are convinced the Holy Spirit is leading each of them but in different ways? Then we obviously have a problem of understanding exactly how the Holy Spirit leads and what He is leading toward. It may be that we need to consider what each other is saying and seek God’s will in mutual prayer. Hopefully we can all improve in discernment together.

Discernment's Center

Why is it wrong for a Christian to claim that everyone is a child of God? After all, we believe one God (in the form of a Trinity of the Father, the Son Jesus Christ, and the Holy Spirit) created the universe and ultimately all humans. What many seem to be missing is that even though we are all created in God’s image, He gives a specific path for acceptance as His children. And this power is given through faith in the Son. Jesus Christ, Who came to the world, lived a perfect life, died and rose for our sins. God wants us to recognize that we sin and that our salvation comes through Christ. And God wants us to tell this to everyone we can--not to leave others in ignorance of Him.

In the Bible, the Apostle John says we are allowed to be children of God if we believe in the Word, Jesus Christ:

But to those who did accept him he gave power to become children of God, to those who believe in his name…(John 1:9-12 NABRE).

In my opinion, this viewpoint can be seen only one way.

There are those who think God will accept everyone. Though we might think that persons who never heard of Christ may be allowed into His kingdom, we must remember that if we have heard of Him we have to evaluate our own faith. If you believe it doesn’t matter what religion other persons are, your own faith and therefore discernment are in trouble. Those who have the opportunity to know Jesus and shrug Him off as one of many choices are worse off than those who have never heard of Him. It is God’s business to decide who comes into His kingdom; it is our job to recognize that for those who do fully know about Him, belief in Christ is the only way to heaven.

This subject relates to another: many people want to see world peace, which we think of as certainly a worthy cause. Especially for those affected by war, it may seem of primary importance. Yet some Christians hold the importance of Earthly peace so high that their worldview seems to put it even above the centrality of Christianity. Here again we have the idea put forth that all religions have the same God, all are children of God. But if you believe Christianity as the only True answer, worldly peace is secondary to evangelization. We must carry the message so all can know Christ, even if it means worldly tensions.

As a Jesuit, Pope Francis claims to seek discernment. Discernment is a method by which a person determines his or her vocation, and also a life-long quest to seek God’s will. The Jesuits are a religious order founded by St. Ignatius of Loyola. In 1522-1524 Ignatius wrote recommendations for spiritual discernment in his book, The Spiritual Exercises (some background and description at Wikipedia HERE. Through this, the members make great effort to tune themselves toward discernment of God’s will.

However, it has been shown that sometimes those who believe they are experts of God’s will have been wrong in their discernment. For example, US Jesuits who ran Georgetown University in the 1800’s owned slaves and then sold these humans to plantation owners of the deeper South in order to financially save the school (Wikipedia HERE). Though slavery was legal at the time, it should not have been considered a moral choice by the Jesuits—those who claimed to know the will of the Lord. Even though the Bible mentions slavery, St. Paul was advising those who had to endure it due to outside influences, not endorsing it as a Christian institution. And the end--a solvent school--did not justify the means. Often when we are confronted with challenges, God will come through if we go to Him and wait for Him. They did not have to own or sell slaves.

Of course, we can't read their minds. Was the president of the university alone somehow deviated from the centrality of Christ? What about others then and there?

The secular Enlightenment was to eventually effect many so-called Christians in disbelieving Christ's miracles and even His divinity, reducing Him to a sage. And Christ centered-ness is just the first step to proper efforts in discernment. Also we can have problems with pride or stubbornness which keeps us from considering other points of view.

Pope Francis seems to want Christianity both ways. He speaks of the need for only Christ for salvation, reported by Ann Schneible,  "Pope: Jesus is the only door to eternal life," Catholic News Agency, April 18, 2016. But at other times he tells everyone that we are all children of God, we all have the same God, or similar phrases (example reported by Elahe Izadi,  "Pope Francis washes the feet of Muslim migrants, says we are 'children of the same God,'" Washington Post, March 25, 2016). The pope holds world peace very highly and wants to see all people get along. But this is simply not the same as putting Christ at the center. The view that it does not matter what you believe is called “Indifferentism” and at least sometimes seems to be held by the pope as well as many other Catholics.

Why is it central to being a Christian to believe in Christ for our Salvation? God gives us free will, and all humans have fallen short of perfection except for Christ. Our own sins should bring us to humility when we recognize them. The Father is just as well as merciful and the imperfection due to sins would keep the sinner ostracized from God's presence. The Father has chosen belief in Christ to be our doorway to Him. As stated above, Christ lived a perfect life and then died for our sins. Jesus should be given the credit for that, just as we want to be credited for our own achievements. But I believe some Catholics, as other Christians, are too casual about sins, the need for Christ for one’s redemption, and about faith in Him in order to go to heaven.

I believe that in order to have right discernment, the central starting point is belief in Jesus Christ as our Savior. Then we can be guided by God to wisdom in other areas. When we really believe this, our love for others should lead us to tell them about Christ, what He did for us, and that we all need to repent and believe that He, and only He, is our Savior.

God's Not Dead 2

I went to see the movie God’s Not Dead 2 (Universal Studios, 2016). I'll abbreviate it GND2. I don’t want to be a spoiler, so I won’t write out the whole plot. But I will tell you that it was about a high school teacher who was sued by the ACLU for answering a question about Jesus Christ, using Scripture, in class.

If you saw the first God’s Not Dead (GND) movie, you will recognize similarities. GND was about a student who was maligned by a college professor because he would not deny God in the classroom. So both movies are about perceived oppression of Christians in academic settings.

Though some may not believe Christians are being oppressed in our country, the credits of the movie show there can be a price to pay when people stand up for what they believe. One real life example I will give is the backlash of the exposé done by David Daleiden against Planned Parenthood. He secretly filmed PP employees talking cold-bloodedly about selling body parts of fetuses, among other shocking images. But it was Daleiden who was indicted in Texas for his undercover work and was recently raided by California DOJ officers, reported by Megan Casella, "California officials seize computers, footage from anti-abortion activist," Reuters, April 6, 2016.

Daleiden's example can be linked with academia because the parts of fetuses go to trained researchers either at universities or in commercial settings. The academic worldview is very often the antithesis of Christianity, even though the medical disciplines do have a noble goal of curing people. They say they are about science and reason and not the "superstitious" religious beliefs. Perhaps that is what justifies their actions in their own minds, and the lines may not always be as clearly drawn as the GND2 movie implies. But cures can be found in other ways and it is imperative that everyone realize the humanity of those who are being killed.

Now, you might say Daleiden was breaking the law in his underground investigation. But consider that a pastor in GND2 says we are in a spiritual war. Non-Christians often see a statement like this as way too overblown. Christians may not always realize where the war is taking place. But the pastor is right, and the people who made the movie, among many others, are in the middle of the battle. When the laws can be unjust, spiritual warriors do not always follow the laws.

Protein Levels

Proteins do much of the work of the cell, the basic biological unit. Proteins are made of sub-units called amino acids, which in turn are made of atoms.

There are thousands of different kinds of proteins. I have posted previously about a set of proteins that work together, called ATP Synthase (ATPS, pronounced ATP sin-thase). The set acts together in this energy production machine. All organisms have ATPS (with the exception of viruses which are parasites and so benefit from ATPS indirectly).

Though I have pictures of ATPS elsewhere, I am putting this picture in my blog because it shows in one view the detail from three levels. The one on the upper left is the whole machine, a picture by David Goodsell at PDB-101 Molecule of the Month, under ATP Synthase HERE.

One of the proteins of ATP Synthase is circled and an arrow points to the box to the right. It shows the makeup of the amino acids in just one part of the machine (represented by their single letter symbols). The sequence for E. coli bacteria can be found at protein database Uniprot entry P0ABB4. As you can see, it is made up of 460 amino acids which have to be in correct order for the ATPS machine to work. (For humans the entry is P06576. Though the number of amino acids is different in humans from E. coli, they still have to be in an arrangement that is functional.) The next box to the left is an image of the atomic arrangement of one amino acid (atoms are represented by their own letters which can be determined by the context).

If you are interested, you can see in a video at a previous post HERE how ATPS operates when protons flow through it because of an electrochemical gradient. The video lasts less than 4 minutes. The molecule that it makes is called ATP, or adenosine triphosphate (ah-den-oh-seen try-fos-fate). This molecule is used to make proteins and DNA among other uses. Here is a picture of it:

Beyond the ATPS, other molecules are needed to set up the proton gradient that makes it work (seen at the same link HERE).

Some proteins can handle a few changes of amino acids, but some positions can't be changed or the protein will not work.

These proteins did not come about by chance, even in billions of years.