Friday, May 29, 2009

LUCA

Before the advent of gene sequencing, the theory of evolution was based on morphology (physical characteristics). Then, scientists developed methods to find the make-up of the gene. The gene is made of a set of 4 molecules which repeat, which we call nucleotides. They have names but we’ll call them A, T, C & G. These nucleotides combine in an order that acts as a code, which is read by other cell units and turned into proteins which do much of the work of the cell.

The National Center for Biotechnology Information (NCBI) is taking the sequences found by researchers all over the world and comparing them. Many of these sequences are done on small organisms of single cells. Bacteria were considered the only organisms to be of one type of cell, the prokaryote (pro-CARry-oat) type. In the 1970’s, scientists realized there was another type of prokaryote, called archaea (ar-KEY-ah). They were considered a separate domain from bacteria and a third one, eukaryotes (you-CARry-oat). The third type is the one in plants and animals, including humans. To make things more complicated, each of the domains have branches, so they need to find common ancestors to the branches for each of the 3.

Unfortunately for the advocates of Darwinian evolution, the results of the sequencing have shown anything but a clear-cut progression from an organism which can be considered the simplest to the next which is more complex and on up to human scale. I will talk more about that next week. But the point is important because it moves the search "back" to a previous ancestor that would have shared genes of all of them and been able to branch off into the 3 distinct domains we see now.

In a paper, "Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea," published by Eugene Koonin et al., they discuss the findings of comparitive gene studies (orthologous means genes that come from a common ancestor. The conclusion for the archaeal branch is:
Genomic reconstructions suggest that the last common ancestor of archaea might have been (nearly) as advanced as the modern archaeal hyperthermophiles.
They estimate it would have had to have at least 996 genes. As they say, it is almost as complex as modern organisms. And archaea are believed to have been present as long as 3.5-3.8 billion years ago. Where then does the common ancestor of all organisms fit? They are running out of back time for all the gene sequences to fall into place, because some scientists think the Earth was too hot for organisms to form until around 4 billion years ago.

Next time, for my last regular ID entry, I will talk about the NCBI results which show the end of Darwinian evolution before it even begins.

Update 1/20/2013: My interest in Intelligent Design Theory (ID) has changed to what is called "Special Creationism," the belief that God created species, including humans, separately and directly. Much of the biological science in ID is similar to Special Creationism.

Tuesday, May 26, 2009

Completely Different


I used to sometimes watch Monty Python on TV. I like silliness to a point. They had some pretty funny skits, but after a while most of them seemed pretty repetitive. They probably realized it themselves, because they introduced some skits by saying, "And now for something completely different..." Now, that was funny.

I feel on the verge of doing something completely different. I started teaching a student ESL, and she works for the diocese. Or I should say overworks. I am going to volunteer my help if I can, perhaps to do some paperwork or whatever she may need.

And, it's summer and around here and that means you get out of the house, do yard work, exercise, just enjoy the sunshine and flowers.

Also, our church is trying to use the Internet more to communicate, but that is stalling a bit. The Pope is encouraging people to use the Internet for outreach (see related CNS article here). I hope to continue this blog and explore different ways I might be effective, locally as well as with the world-wide potential the web gives us. There is a need, I think, at the local church level for organization and a place to share ideas and concerns. I'd like to see what else is going on in our area and what might be done.

I've done a lot of work on Intelligent Design Theory, both learning it and trying to teach it to others. I have used this blog to try to show the complexity of biological life, and I will probably once in a while get back to that theme (and I'm not quite done yet--I'll have a few more weeks of entries). It is a very exciting time in biology, but the complexity makes the facts difficult to teach. And there is only so much you can teach by writing. Most people would need person-to-person instruction to learn it well or even to "get it" at all, but there do not seem to be enough interested persons in order to organize local classes yet, or perhaps I am not finding them. I think interest will increase as more information surfaces, but I don't know how soon it will happen. I hope to be able to give lectures on ID once in a while as I may encounter interested people, but I am finding I don't want to devote all my time to it anymore.

I still have other issues I want to research and write about. There is still much to do. And so, I am moving on and yet staying on. I am grateful to God for the journey.

Update 1/22/2013: My interest in Intelligent Design Theory (ID) has changed to what is called "Special Creationism," the belief that God created species separately and directly. Much of the biological science in ID is similar to Special Creationism.

Friday, May 22, 2009

LUCA to come


I've been really busy this week, so I'll just give you an intro into my next Intelligent Design theme, which will be related to some in the past. Of course, biological life is all intertwined, but there are distinct categories we work with.

I've had a series about "Origins" which started here. I talked about some of the issues of naturalistic, materialistic theories for the beginning of life. One concept I mentioned was the "Last Unknown Common Ancestor," abbreviated LUCA (here). Though the term does not in itself indicate a very first organism, it heads in that direction. It includes research into what genes and proteins the ancestors of present-day species would have needed in order for the organisms of today to be what they are. It considers the number of possible offspring that a certain organism could have through the generations and how much the inner workings could have changed in that time (on a natural basis).

In fact, I've found some very interesting research on this, and hope to get into the details by next week.

Update 1/20/2013: My interest in Intelligent Design Theory (ID) has changed to what is called "Special Creationism," the belief that God created species, including humans, separately and directly. Much of the biological science in ID is similar to Special Creationism.

Tuesday, May 19, 2009

Angels & Directors

Since the movie "Angels and Demons" has opened, I thought I would make some comments about it.

I have not read the book by Dan Brown or seen the movie directed by Ron Howard and starring Tom Hanks, nor do I have intentions of doing so. But I have read reviews and seen the History Channel's "Angels and Demons Decoded," which spent two hours describing the novel's claims and supposedly secret codes.

The main theme is that the Church has been (and still is) in conflict with modern science. The presumption is that science threatens the message of the Church: that God made heaven and Earth and the creatures therein.

The history of Galileo and Copernicus are supposed to be our basis for learning about past mistakes. Both scientists claimed the sun to be the center of our solar system (called heliocentrism, he-lee-oh-CEN-trism). The Church at the time did not accept this scenario. But those who would point that out in support of the present-day equivalent of the problem, the Theory of Evolution, are missing the greater lesson. The Church at the time was following what most scientists believed. Copernicus and Galileo were among a minority of scientists coming to this conclusion, building on increasing evidence. These two scientists were overturning the theories held by those of the Greek Aristotle and Roman Ptolemy who both had their own logical reasons for thinking the Earth was at the center. The majority of scientists believed these old theories. Then came the telescope, an instrument with which Galileo could be much more sure of Copernicus' idea of heliocentrism.

So, the scientists of today who recognize the legitimacy of Intelligent Design Theory are actually much more similar to Galileo and Copernicus than the ones who stubbornly hold onto Darwin's theory no matter what new experiments reveal. The IDists are in the minority, but that doesn't mean they are wrong.

Church authority are not scientists. They weren't then and they aren't now. Neither are movie directors or fiction authors (at least most of them). Brown doesn't even care that his "anti-matter" bomb is totally bogus scientifically (a comment about it here at CERN). Why should we expect expert statements about the scientific status of evolution from the Pope? Actually, I think Pope Benedict has handled the situation pretty well. He has sponsored intellectual inquiry into the subject in one of his annual meetings with former students. A book about that event, Creation and Evolution, (Ignatius Press, 2008) compiled by Stephen Horn, was reviewed by me here. As I said in the last of 4 posts about it,

The Pope thinks that although science has discovered great things, its "findings lead to questions that reach beyond its methodological principles and cannot be answered within science itself" (163).

Directors such as Howard have great influence on our culture. He is probably sure he is promoting the cause of true science. How ironic that he follows the crowd whose faith in "old" science actually impedes the correct analysis of new discoveries.

Sunday, May 17, 2009

Sunday Snippets--A Catholic Carnival 2

I am linking again to RAnn's blog for Sunday Snippets in which she lists links to other Catholic blogs. I have enjoyed reading her blog in the time since she invited me to join her list of Sunday Snippets. She reads and reviews religion-related books, both fiction and non-fiction. Her blog is here and the new connection to Sunday Snippets is here.

Friday, May 15, 2009

Anaerobics


In the last few ID posts, I showed some proteins from cell membranes. The point was to see that the cell needs some rather complicated structures to keep charged particles and water at a balance so the cell doesn't explode or collapse. I want to tie that into the speculations of materialistic origins of life.

To the right is a protein from a bacteria named Desulfovibrio Vulgaris (NCBI taxonomy ID 882). I show this to you because of the evolutionary story that the first creatures on Earth were anaerobes (pronounced AN-air-robes). These creatures did not need oxygen to breathe. It is maintained that atmospheric oxygen was not available at first in sufficient quantities. The materialists believe that because if oxygen were available, it would keep organic molecules from forming, and thereby life itself could not start on its own. So the first cells were supposedly anaerobic. (I have seen speculation both ways on whether there was oxygen in the very early atmosphere but will not get into it here). The oxygen was theoretically produced by the first living organisms, and then later organisms adapted to the oxygen in the atmosphere. The protein at right, from Uniprot P45574 and RCBI PDB 2v4j is part of the pathway that uses a sulfur-containing molecule instead of the ones used in oxygen-type respiration. It is made of several types of protein chains, totaling over 900 amino acids.

A paper about the very beginnings of life, "The Origins of Archaea: a state of the art," speculates on the first organisms. The paper is by Girbaldo and Brochier-Armanet, published in Philosophical Transactions of the Royal Society, May 9, 2006. It is found in full through PubMed Central here. Archaea are one of the 3 domains, or groups of life, based on cell construction. The other two are Bacteria and Eukaryotes. The article includes all three domains in its analysis (although is mostly about Archaea). It states that though a certain type of Archaea (methanogenic) were previously thought to be the first organisms, their whole-gene sequences do not bear out that theory. Now it is thought that anaerobic bacteria which have this sulfur-type respiration were among the first (see Section 3, "How Old," in the paper). So this is why I looked up this type of organism.

Interestingly, this bacteria has the complete proteome available at Uniprot here. It has 3,517 proteins listed. Some of them are not complete in themselves. They have to fit together to make the protein work. This does not diminish the effect of the number, however, since some of the types of proteins are used several times in the same protein machine. For example, ATP synthase as pictured in a previous post has several types of subunits, some used as many as 12 times in the same structure. You will notice in the complete proteome that D. vulgaris also has an ATP synthase structure.

The type of respiration in anaerobes may be different, but the first organisms still needed complex structures for energy production, cell membrane transport and other cell activities. The picture to the left is not from D. vulgaris, but shows a Sodium-hydrogen type cell membrane protein that the organism does have. This is also made up of hundreds of amino acids in specific sequence in order for them to fall into the shape they need for function.

So, you can see that even the very first types of organisms needed complex types of proteins in order to function. It doesn't really matter whether they used oxygen or not. It may sound like an organism is simpler if it doesn't use oxygen to breathe, but it still needs many metabolic pathways in order for it to manufacture its own DNA, RNA, proteins, and other structures so that it can support life and reproduce.

Tuesday, May 12, 2009

Deacons 2


The picture to the left depicts the Apostle Paul with Phoebe. She is mentioned in the Bible in Romans 16:1-2. (I was pleased to discover this morning that the USCCB website has the full text of the New American Bible.) Paul asks that she be received by the Christian community to whom he is writing and given all the help she needs, since she was a Christian minister. Many have said she was a deaconess.

The Roman Catholic Church had permanent deacons in the first millennium, but the practice faded and the diaconate became simply a step along the way for men to become priests. There is evidence that the deacons were both men and women. The Council of Chalcedon in 451 has a section which states: "A woman shall not receive the laying on of hands as a deaconess under 40 years of age, and then only after searching examination" (from: New Advent, Church Fathers, Council of Chalcedon, Canon 15).

The second Vatican Council in 1964 spoke of the need for the office to be restored "not for the priesthood but for the ministry" (Lumen Gentium, 29). The tasks of the deacons include administering Baptism and the Eucharist, presiding over worship and prayer, officiating at funeral and burial services, and visiting shut-ins among other activities. Pope Paul VI restored the office in 1967 on this recommendation of Vatican II. The deacon is ordained by the bishop of the diocese. The USCCB has a Diaconate section on its website with the online National Directory for the Formation, Ministry and Life of Permanent Deacons in the United States.

Phyllis Zagano, author and university professor, wrote about the restoration of women to the diaconate of the Catholic Church in her year 2000 book, Holy Saturday. She has a vast knowledge of Church history and law and sets out a very good argument for this restoration. As she says, women are doing the work of the Church but "there is still no way for the bishop of a diocese, on behalf of the local church, to formally call forth women servants of the Church, to recognize and to ratify their service through orders" (p. 69). Wikipedia also has a lot of information on the subject of Deaconess, which I will not re-write here but direct you there if you are interested.

Catholic Online has an article about a homily given by Pope Benedict over the weekend at a mass in Amman, Jordan. He is visiting there on his week-long pilgrimage of the Holy Land. He exhorts others to pay attention to the "prophetic role" of women. Well, in the Old Testament lands which the Pope visits, many prophets cried out and no one listened. Women prophets cry out today. They beg, they plead, they pray, but the Church authority does not listen. They are saying: women are to be treated equally. Sacraments should not be withheld from women because of their gender. Women should be ordained!

Friday, May 8, 2009

Cell Membrane 3


The picture at left is a membrane transport protein known as a sodium-potassium pump. Details are found at the OPM site of University of Michgian. The horizontal red and blue lines represent the cell membrane outline.

This protein, or actually set of inter-working proteins, has about 2500 amino acids. It is necessary for the cell to be able to pump out positively charged sodium particles so that the cell doesn't become too attractive to water, which can move in by osmosis and explode the cell. There are many negatively charged proteins and positive particles inside the cell, and this pump keeps the positive ion level down. The action of the pump is part of what is called active transport, when particles are moved against a gradient and/or are unable to diffuse through the membrane. More information can be found at the Wikipedia site for Sodium-pump.

There are other reasons for a sodium gradient, such as stimulation of nerve cells. These cells must move ions quickly in order for them to pass a charge along their membranes from one end to the next and from one cell to another. Different cells have specialized needs and the membrane proteins must be able to handle them. Muscle cells need calcium in order to contract. Cells must move food in and waste products out, and must respond to changes in levels of hormones in the blood stream. All these take individually specialized membrane proteins, since the rest of the membrane will not allow large proteins and food in or out.

There have been discoveries of proteins which are completely different and yet have some of the same properties. They are composed of different sets of amino acids (the building blocks of proteins), yet they fold in similar ways, which allows them to do similar work. However, folding itself is rarely found in randomly arranged amino acid sequences, as reported by protein laboratories in papers such as this by Moffet and Hecht (the introduction is quite interesting). Therefore, though the numbers of proteins which can carry on a specific job may increase, the total is still vanishingly small. The calculations of just how many are being worked upon now by many on both the materialistic and design advocate "sides." Considering the low probabilities (such as 1 in 10^65 viable for a protein of 100 amino acids calculated by Hubert Yockey), the numbers would have to be amazingly large to make a dent. That seems unlikely since many proteins are believed to be very close to the same as they were at the very start of life. (On a different note but related: many proteins are being found unique for particular species.)

Thursday, May 7, 2009

Sunday Snippets--A Catholic Carnival

I usually post on Tuesdays and Fridays, but yesterday I was invited to send my address to a Catholic blog by RAnn (see comment in previous post). She collects links to Catholic blogs, and I am hoping I figure out how to connect with them today. She lists other blogs on what she calls a "meme," and that link is here. I have already checked out some of the blogs listed and enjoyed seeing the variety. Her own blog, This That and the Other Thing, features book reviews and games. RAnn invites anyone, whether they have a blog or not, to come and see!

Tuesday, May 5, 2009

Latin America

Since I am on the subject of changing subjects (see last week's Bishop Lugo 1), I will talk about one of the other main interests in my life: Latin America. I ended up studying veterinary medicine in college, but for some reason always longed to go and live in Central America. I love the Spanish language, and in fact planned to use my veterinary medicine there. But, life happens and I got married (to a previous husband). I sometimes wish I had taken Latin American studies in school. But of course, one can learn on one's own. I read a lot about the history, and watch the news on Spanish TV. I've been to Mexico 4 times now and El Salvador once, with future plans to return.

Who knows why we have the interests we do? We are born that way, I guess, with some input as we grow. I was fascinated by the stories of Latin America on World News as I started studying Current Events in high school. I also took four years of Spanish then, and took a college semester just a few years ago. The countries which have Spanish as their official language are in dark blue on the map, with light blue showing a significant population speaking it in the US and dark green the same for Brazil. (Red and pink stand for French, and light green Portuguese.) I think it is well worth-while for all of us in this hemisphere to speak at least a little of Spanish. Our teacher in college also stressed culture so that we'd have some understanding of what is important to persons from particular countries.

I've found an outlet for my interest in volunteering for English as a Second Language (ESL). I helped one woman go through all her ESL study books, and now I will start this week on helping another to try to get her US citizenship. I look forward to learning what the English requirements are, since I've been wondering about that for a while.

And so I go on with my rather motley group of three main interests: Intelligent Design Theory, Latin America and Women's Ordination (at least as Deacons) in the Roman Catholic Church. Of course, underlying everything in my life is a love for God and His Church and people.

I used to think I could "get somewhere" if I'd have only one main focus to concentrate upon for a career, but I've found this is nothing I can change. I don't think it's just a matter of discipline, because Lord knows I've tried. I can't help getting internally upset if I don't have enough time to pursue a particular question I want to research or do an activity I think is important, and I only have so much energy. I have moved on from Veterinary Medicine to writing, and I guess it serves a writer well to have varied interests. But sometimes I wish mine would mesh a little better. Anyway, I will sometimes be commenting on Latin America and sometimes on Women's Ordination, so if you want to read only about Intelligent Design Theory, click the ID link under topics in the right column. Otherwise, perhaps you may enjoy broadening your horizons by sharing in varied topics with me.

Monday, May 4, 2009

Deacons 1


To the left is a picture by Jean Fouquet of St. Stephen. I assume Stephen is the one holding the Bible and stone, since he is one of the first Christian deacons and also the first Christian martyr (by stoning). I had not heard of Etienne Chevalier, but apparently he wrote a book of hours, which is a medieval illustrated devotional.

Deacons were assigned by the original apostles to make sure that the goods of the early Christian community were distributed fairly. The Christians gave their worldly goods to the Church and tried to live equally. But widows of Greek-descent Jews were grumbling that their needs were not met (Acts 6). The apostles realized that they couldn't both preach and be food distributors. They therefore assigned the tasks of stewardship to others.

I didn't mean to post this blog today, but am having some technical difficulties saving it, so I'll keep it short and continue history of Deacons next week. Tomorrow I'll tell you about one of my other main interests, and we'll go from there.

Friday, May 1, 2009

Cell Membrane 2




The lipid bilayer of the cell membrane allows only a few types of molecules through it, such as water. Because of the biochemical qualities of the inner fat layer of the membrane, charged particles have more trouble getting through than neutral ones. Water is able to go through with relative ease. This is not fully understood, since it does have some polarity. In any case, the membrane needs to have other ways to get ions, atoms and molecules from the outside in and vice versa.

It does this by specific proteins which regulate these things individually or in sets. Above is a picture of a protein complex that regulates potassium, from the RCSB Protein Data Bank . The gray band in the picture is the cell membrane. Several proteins sit right in the membrane and act as a filter against everything but potassium. Then, the channels below leave potassium in or not depending on the cell's needs. The levels of ions such as potassium and sodium are finely regulated to fit to the metabolic needs of the cell. There are large differences between the levels of ions on the inside and outside of the cell.

The pictures at left from RCSB are channels as viewed from the top. Links are available through the protein complex link above.

Next post: more membrane transport proteins.