Friday, January 29, 2016

Bioethics

On Jan 28, Pope Francis met with a group from Italy concerned with bioethics (link HERE). He calls for the respect for human dignity from conception to natural death. In US bioethics, the “bio” part is clear but the “ethics” not so much.

The National Institute of Health (NIH) has a webpage for their Department of Bioethics (link HERE). However, they also have a webpage for their Human Stem Cell Research (link HERE). Dr. Francis Collins, director of NIH, has promoted human embryonic research. He has made presentations to members of congress (link HERE). Previous protections for embryos were reversed by Barack Obama in 2009, affecting funding for NIH research (link HERE).

Dr. Collins also founded Biologos (link HERE). This organization announces itself on its website by saying, “Biologos Invites the Church and the world to see the harmony between science and biblical faith as we present an evolutionary understanding of God’s creation.” Now, this statement could have quit right after “biblical faith,” or have said that the understanding comes through physics or through biology, but how does it continue? The group presents an evolutionary understanding of God’s creation.

Is there a link between believing in random evolution and accepting research on human embryonic stem cells and fetuses? I hope I am not insulting the reader, but I believe I see this connection. Perhaps complete randomness implies a slight lowering of human value, enough of a lowering that humans in the womb are expendable. If you do not agree, let me know. But please think it over first.

Monday, January 25, 2016

Orphan Genes

Scientists started comparing whole genome sequences of various species in the 1990’s. Genes that are only found in one or very closely related species are called unique, de novo, ORFan or orphan genes. The amazing thing is that the more they compare species, the more unique genes they find. These genes make up from 10-20% of each organism’s whole set (percentages given by Dr. Ann Gauger here). These unique genes are so different from each other that the chance they could have come from an evolutionary sequence is vanishingly small. This is, for one reason, because there could have been no more than 10^50 organisms on Earth so far even if the Earth is very old. The unique genes are statistically so far apart that even this many organisms are not enough to sort through the various possibilities.  (And only one in about 10^65 proteins is functional. So the sorting of proteins for functional ones makes evolution by chance look pretty much impossible.) In contrast, if all genes (and corresponding proteins) were closely related and in obvious sequence in species, Darwin would have been proven right.

Eugene Koonin is Senior Investigator of comparative genomics at National Center for Biotechnology Information (a division of NIH) and has written many articles. So he is on the front lines of comparative genomics. He and Yuri Wolf wrote an article in 2008 called Genomics of bacteria and archaea: emerging dynamic view of the prokaryotic world. They found there were some proteins common to many species of bacteria and archaea (one-celled organisms different from bacteria). But what surprised them was the vast amount of variety between species and the unique genes. Koonin has become part of a movement to find other explanations for evolution instead of neo-Darwinism called the Third Way of Evolution. The "evolution" part is because he is committed to evolution. But these findings of comparative genomics also support direct creation of species.

An article by J. Muller et. al. called, eggNOG v2.0 compares various species. In the diagram you can see species names in the middle with radiating lines that go out to colors of the graph. The green and orange represent genes which are related, but the outer gray areas are orphan genes which do not match other species.

A more recent article has reinforced these findings. The researcher Jorge Ruiz-Orera and his group were looking for unique human and chimpanzee genes and found them. Their author summary starts:
For the past 20 years scientists have puzzled over a strange-yet-ubiquitous genomic phenomenon; in every genome there are sets of genes which are unique to that particular species i.e. lacking homologues in any other species.
Homologues are related genes. As stated above, these unique genes cannot be explained by the supposed machines of evolution: mutation and selection. The complete published paper can be found online at PLOS Genetics here:

http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005721

On a related subject, a problem in the past was that in comparing genes, scientists used genes they already had to see if they were in the other organisms. This left sequences that did not match out of the loop of potential genes. However, they have begun to use other criteria, such as start and stop sequences, to now identify more non-matching areas that look like genes. This is promising to show even more unique genes.

Saturday, January 23, 2016

Conscience and Religion

We cannot read the minds of people of other religions. When addressing one or another, we might wonder what their consciences are telling them about their sins. This understanding that everyone sins is crucial to Christianity. Jesus Christ, Son of God, came to us to atone for our sins. He lived without sin and died in our place so we humans would be acceptable to God and therefore able to live in heaven with Him (God being in the form of Father, Son and Holy Spirit). Jesus told us that if a person believes in Him, s/he will be saved. He didn’t say it doesn’t matter what you believe.

Yet we have people around us who do not believe in any religion or believe in a different religion and seem to not be bothered by their conscience. Others believe they might have done evil but think their own religion answers to it, such as Karma in Buddhism. And there are others who do believe in Christ that don’t seem to feel urgency to spread the word about Christ.

Christians believe it is the Holy Spirit who convicts people of sin. Jesus says in John 16:7-8 (NABRE):
7 But I tell you the truth, it is better for you that I go. For if I do not go, the Advocate [Holy Spirit] will not come to you. But if I go, I will send him to you. 8 And when he comes he will convict the world in regard to sin and righteousness and condemnation…
I think that most people have a conscience whispering somewhere in their brains. The Catholic Church respects the free conscience of persons, which can be seen in this section of the Catholic Catechism on conscience in making moral decisions (Moral Conscience Section of the Catholic Catechism, link is HERE):
1782 Man has the right to act in conscience and in freedom so as personally to make moral decisions. "He must not be forced to act contrary to his conscience. Nor must he be prevented from acting according to his conscience, especially in religious matters."
I do think humans are made for the Truth, although sin and fallen nature get in the way. In this Truth is the desire to do good. Certainly when a person does wrong, a healthy conscience makes him/her uncomfortable. But what about faith? The same section listed above:
1787 Man is sometimes confronted by situations that make moral judgments less assured and decision difficult. But he must always seriously seek what is right and good and discern the will of God expressed in divine law.
1788 To this purpose, man strives to interpret the data of experience and the signs of the times assisted by the virtue of prudence, by the advice of competent people, and by the help of the Holy Spirit and his gifts.
(More on conscience is found in the Vatican II Declaration on Religious Freedom, linked HERE).

As it says there we should seek the Holy Spirit and His gifts, some of which are right judgment, understanding, knowledge, courage, wisdom, reverence and awe and wonder in His presence. Even for those who are not familiar with Christianity, they can seek Him by praying that He come to them. The Holy Spirit then draws them to the true God. For them, it can be the start of an overwhelmingly lovely relationship.

Thursday, January 21, 2016

Catholic Answers Forums

I have been posting on Catholic Answers Forums (CAF) a little bit and I thought I’d put some of the issues I follow there on my blog here. If you want to check out CAF, you can click the link HERE.

We’ve been having an interesting time talking with people from various faiths. Buddhists and Hindus among others have had input on our board. I’ve been in a discussion that’s been going on for a while that is called “3000 gods but only yours exists.” Apparently someone had an atheist friend say that to them in a sarcastic way and the person asked for ideas of what to answer back. The thread is still going after 16 pages of 15 comments each but the original poster is probably long gone by now. Anyway you can get to the thread by clicking HERE if you are interested in seeing it.

One issue brought up was whether you have to be a Christian to go to heaven (at least our idea of it). This is a contentious issue even among Christians. The Vatican II document Lumen Gentium addresses this. However, this document was a source of confusion and even today we have liberals and conservatives arguing over it. It mentions Jews and Muslims as being related to the people of God. And yet it warns us that in the end:
But often men, deceived by the Evil One, have become vain in their reasonings and have exchanged the truth of God for a lie, serving the creature rather than the Creator. Or some there are who, living and dying in this world without God, are exposed to final despair. Wherefore to promote the glory of God and procure the salvation of all of these, and mindful of the command of the Lord, "Preach the Gospel to every creature", the Church fosters the missions with care and attention. (Link is HERE.)
Concerning the confusion, in 1999 Josef Ratzinger, who became Pope Benedict XVI, wrote a Declaration called Dominus Iesus. In Section 5 he states:
5. As a remedy for this relativistic mentality, which is becoming ever more common, it is necessary above all to reassert the definitive and complete character of the revelation of Jesus Christ. In fact, it must be firmly believed that, in the mystery of Jesus Christ, the Incarnate Son of God, who is “the way, the truth, and the life” (Jn 14:6), the full revelation of divine truth is given: “No one knows the Son except the Father, and no one knows the Father except the Son and anyone to whom the Son wishes to reveal him” (Mt 11:27); “No one has ever seen God; God the only Son, who is in the bosom of the Father, has revealed him” (Jn 1:18); “For in Christ the whole fullness of divinity dwells in bodily form” (Col 2:9-10). (Link is HERE.)
It is our obligation as Christians to proceed under the understanding that Christ is absolutely necessary for our entrance into heaven. How He will judge others of different faiths is His business. Our job is to witness to Christ in every way possible, including the effects of His presence, along with the Father and Holy Spirit, in our lives.

Tuesday, January 19, 2016

One Post at a Time

It’s been quite some time since I’ve added a post to my blog. I seemed at a crossroad when I finished my book, Biotech Swirl, and didn’t know if I wanted to keep writing the blog. Though it might not seem like a monumental decision, I felt I’ve had to pray about it. My husband’s health is not that good and I might have to drop the blog again if I get too busy in care-taking.

I'm not sure I’ve had any profound insights from my prayers except that I realized I am living one day at a time, so perhaps I should just approach my blog one post at a time. I kept updating the last post so I might as well write new ones. I had been doing regular monthly posts for a while but now I will just write when I feel moved to do so and see how it goes. If you are reading this, thanks for your patience while I get myself together.

I'm still going to Catholic Answers Forums and sometimes post there. You can get to it by clicking here if you are interested (or perhaps you already are familiar with it). They have a lot of good discussions there and I think the website is very well done. In fact, it was in reading the discussions there that my fingers started to itch to write again.