Should YECs do a Phd?

It has been a while since I have posted something on this blog and I have decided that it was time to write another blog post about a big question that has bothered myself for a long time.

As regular readers of this blog know, I am fairly convinced that the earth is only 6000-12000 years old, which is obviously not in line with the modern scientific world-view. Creation and especially advocating the young-earth creationistic position is not done in mainstream science.

For me and other christian biology students it is often a big question whether we should pursue a academic carreer. And it is not difficult to see why. When almost all people are convinced of the evolutionary framework it is difficult to reconcile one’s faith-based position with that view on science. There is a league of scientists around that would say that evolution-deniers are not suitable to walk on an academic carreer path.

But on the contrary of those often heard statements about pseudo-science, I actually know several christian students which are actively involved in research related to biology and genetics.

…But my brain is still going around and around in circles whether I should pursue an academic carreer and start with a Phd. 

As of know I know all arguments for and against it, but I am curious about your opinion about this. Please enter a reply with your opinion about this case below!

A response to Tyler Francke

Often young earth creationists (YECs) are ignorant and stupid in their reasoning and do not think about what arguments they give in advance of the creation perspective. Let’s be clear, for me being a  YEC, this really is not something of which I am proud to say it.

But it is more than true. As creationists we could learn a thing or two about humility and respect towards the beliefs of others, which often are in great contrast with our own beliefs.

Recently I read an article that was posted on the website www.godofevolution.com, which is a website that tries to argue in advance of harmony between evolution and christianity. This website was founded in 2013 and is led by Tyler Francke and in one of his articles he tries to explain why believing in a young earth has seriously bad theological implications.

He names three theological implications (which I have summarized below). For a more extensive writing you should read the original article by Tyler Francke:

  1. God is a liar: The YEC position must assume a deceptive God because most of the scientific evidence is against the YEC position (radiocarbon, Vredefort crater, continental drift, Y-chromosome ancestry, etc).
  2. Faith  is unnecessary: God puts a premium on faith in the Bible. There is no reason to have faith, because there is no power in objective facts. The argument is that YEC don’t have to believe, because they claim to have reasonable objective facts.
  3. Unbelievers must be avoided: YEC creates a gap between believers and everybody else. So in other word, YECs do not see the great commission as of importance.

I have thought about above stated theological implication, whether I should comment on this or not, because to me it is quite obvious that those implications are not true and based on unreasonable arguments. So in short, I could not pass on my moral obligation to nothing and the comments below are my own reflection and commentary on the ‘three serious theological implications of young earth creationism’.

Last year,  I read an article by Todd Wood about ‘surrender‘ and I really encourage you to read this essay because it conveys an important message about how the conversation should go between evolutionists and young earth creationists. 

I quote:

I think that the God who created this universe is still God enough to help us work out our differences. I know that His Word will accomplish what He sends it to do. He doesn’t need my help to get the point across. He doesn’t need me to defend Him. If we believe that God is sovereign – if we really believe it – then we really ought to relax and let Him do His work. Surely He can sort out all these debates when we seek His guidance, but if we try to control things ourselves, to selfishly get the other side to admit we’re right, we really will bring shame on the gospel.

I confess that these acts of surrender will not be easy. I really do want to recognize God’s sovereignty and to give up my vain desires, but as a young-earth creationist, I have grave concerns about the mixing of evolution and Christian theology. I feel like I need to do something, but maybe that something is surrender. Maybe I should cast myself at Jesus’ feet and ask Him to help my unbelief. I hope you’ll do the same, and perhaps together we’ll see God move in a remarkable way.

I think He’d like that.

That is  the starting position which I submit myself to as a young-earth creationist. But what about the ‘seriously bad theological implications’ that Tyler Francke is talking about? Should we surrender, and admit that those are true? Or should we engage in an conversation about the contents of the implications? The last option is the one that I have chosen.

The first theological implication would be that God is a liar, because the scientific facts are mostly against the YEC position. This argument is based on the assumption that the theories that are made are objective and true. But there’s also faith (I will talk more about faith when I review the second implication). My faith in an inerrant Scripture is not based on facts. It is because I believe that our Creator has created the world in six days and rested from His works on the seventh day. And what is more important? What the Scripture says, or what scientific theories say?

The view that humans are fallible, while God is infallible, is not a new view, but we can already see that in the first pair of humans. We are not perfect, but God said to Moses that the earth is created in six days,  as we read in Exodus 20:11.

Ex 20:11 For in six days the LORD made heaven and earth, the sea, and all that in them is, and rested the seventh day: wherefore the LORD blessed the sabbath day, and hallowed it.

Does that make God a liar? If God has said it, we ought to believe it or not?

The second theological implication is that faith is unneccessary. Talking about objective facts is dangerous, especially when in the first implication was stressed that God is a liar, because the scientific facts say otherwise. Abraham is a man who is remembered because of his strong belief in God. According to the Bible he was the MRCA of the Jews and the Arab people.

I definitively agree with the statement that there is more power in faith than in reason. As said before, humans are fallible. But what I do not agree with is the statement that YECs do not need faith. They need it, but seek confirmation in science or theories and observable facts around us. That is quite the opposite of what Tyler Francke is talking about.

The third theological implication is that non-believers must be avoided. Creationists often say that evolution has deleterious effects on belief and worship of God. That’s true, and if people claim that, they should have an explanation with solid arguments for saying that. But to say that YECs do not take the great commission seriously is simply not true. I have heard YEC speakers which talked in a humble way about their beliefs and faith in Christ to a large sceptical audience. I have spoken with other YECs who are very active in reaching out to non-believers.

Creationism does not teach that non-believers should not be reached. There is no doctrine that tells this, and there is no YEC who has ever said that reaching out was not important. This is not a consequence of YEC beliefs, and it really cannot be stated that creationism says that other people should not be reached.

Surrender is something that asks a lot and I admit that I have often little patience for surrender. That is an observable fact in my life. And that’s maybe also why Tyler Franck wrote this article, because we as YECs are  often not good at surrendering ourselves. That is not a good thing and we should be ashamed at ourselves.

In order to advance the conversation about evolution and creation, surrender is needed. I once talked to fellow students about my creationist beliefs, and they asked me what I thought of bold claims that creationists often make, and I replied that I could not see another option than creation,  because of my faith, but that my faith also requires respect for people who tend to disagree with my position on evolution.

 

 

The International Conference on Creationism

As many creationists will know in August 2013 the International Conference on Creationism is scheduled. This conference is according to their site acclaimed in creation world.

The ICCs have been recognized as the world’s premier gathering of creation researchers and have, since the first conference in 1986, served to greatly further the creation model of origins.

The last ICC has indeed given a spark to the creation debate when Todd Wood published his AGEing model for biological diversification. The second thing of notice is the presentation that John Sanford gave on ‘using numerical simulation to test the validity of Neo-Darwinian Theory.

Regular readers of my blog know that biological diversification is a theme on which I frequently blog (For example my post on network analysis and creationism or Evolutionary stasis and abruptness).

I am quite curious about what the coming ICC will bring for creation biology and related fields. Although I am not able to attend this conference, this will be the major event for creationism and my anticipation is high.

When I look at the confirmed speakers I see several presentations that interest me:

  1. A Creationist Perspective on the Origin of Pathogenic Vibrio Choleae and Vibrio Cholerae Toxin by Joe Francis and Todd Wood. 
  2. The Fossil Record of Angiosperm Families in Relation to Baraminology by Roger Sanders.
  3. Mitochondrial DNA Analysis of Three Terrestrial Mammal Baramins (Equidae, Felidae, and Canidae) Implies an Accelerated Mutation Rate Near the Time of the Flood by Todd Wood
  4. The Fossil Record of Angiosperm Families in Relation to Baraminology by Roger Sanders
  5. Baraminological Analysis of Jurassic and Cretaceous Avialae by Paul Garner, Todd Wood and Marcus Ross
  6. Chromosome Number Changes Within Terrestrial Mammalian Families by Karen Bedinger
  7. The Chasm Between the Human and Chimpanzee Genomes: A Review of the Evolutionary Literature by Jerry Bergman and Jeffery Tomkins
  8. Using Numerical Simulation to Better Understand Fixation Rates, and Establishment of a New Principle – “Haldane’s Ratchet” by Christopher L. Rupe and John C. Sanford.
  9. A Review of the Last Decade of Creation Biology Research on Natural History, 2003-2012 by Todd Wood.
  10. Whatever Happened to Darwin’s Tree of Life? by Paul Nelson
  11. New Research Evaluating Similarities Between Human and Chimpanzee DNA by Jeff Tomkins.

And there is one I am extremely interested in, because I really do have my reservations by statistical baraminology:

  1. Australopithecus Sediba, Statistical Baraminology, and Challenges to Identifying the Human Holobaramin by Todd Wood

Stay tuned for more updates about these subjects. In the next months, and definitively in August I will blog more about this conference and related topics.

on ENCODE & telivision sets, apes, silence and Dawkins

It is rather an odd title for a blogpost, but I felt like it needed that. Last months were busy months and it really was not that I did not like my readers anymore, but just that it was a busy period with a lot of finishing of projects and things like that.

But in fact I think that an update is needed desperately on this blog. Do not expect new content in this blog, but it will most certainly be about what others have blogged about and about what I have thought about related to existing posts on this blog.

  1. Encode revisited: Last year I blogged about the ENCODE results which showed that presumably a large part of the genome was functional (according to their definition), and I want to point out to an paper that was published in February which tries to debunk the claims the the ENCODE project made. I don’t agree with all of the paper, but that is something which is more suitable to a stand-alone blogpost. 
  2. Similarity between chimps and humans: In the Answers Research Journal (ARJ) a study was published that genomic similarity between chimps and humans is only 70% instead of the 98% to 99% which is assumed by most of the scientific community. Dr. While (YOUNG-earth creationist) has blogged about it. But that’s also more for another blogposts, because I tend to almost agree.. (again)

That were the pieces where I did not completely agree.

  1. On the Colossian Forumreflection article was published by Daniel Camacho who wrote about the virtue of silence based on the works of St. Thomas Aquinas. This article has my recommendations.  
  2. Some time ago a debate was organised between Rowan Williams and Richard Dawkins.The subject of the evening was whether religion has a place in the 21st century. I believe it does, as does Rowan Williams.

Judging Judging

And this is for fun (at least boring fun)

In a few weeks I will have more time to blog, but those posts will still be irregular.

[edited: Dr. While is not an old-earth-creationist, but firmly in the young earth creationists camp.]

Bryan College dropping support for Center for Origins Research

Bryan College has decided to stop funding the ‘Center for Origins Research’, which is not a good thing for creationist research.

Todd Wood himself, describes his job as:

I have long known that CORE is a luxury for a small, Christian college.  In fact, every time I described my job, people were always shocked to hear that an undergraduate institution like Bryan employed faculty to do research (my teaching load is a quarter of a standard teaching load).  I also long feared that financial hardship would spell the end of CORE, since luxuries are always the first to be cut from a budget.

Bryan College will support CORE until end June, and I sinserely hope that Todd Wood, his wife, and Roger Sanders find another way to secure funding for CORE or to obtain other jobs.

Although I not always agree with Todd Wood, he is one of few people who try to justify a creationist model by reason and science. That’s to be applauded.

Without Todd and others, creation biology wouldn’t be what it is today, and I hope that he will find a way to continu his research.

At the Panda’s Thumb Nick Matzke (who makes his career by dismissing creationism and ID ) also provides some commentary.

If you have any thoughts about this, please let me know in the comments.

Joachanan

Edited: 23-1-2013 because of interpretation mistake

Network Analysis and Creationism

Biological networks are hot these days in genomics, genetics, and bioinformatics. It’s obvious that with the rise of the modern-day ~omics technologies huge amounts of biological data are available for biologists (for example gene expression data, protein, metabolites measurements). In the living cell those key components of life interact with each other and form biological networks.

Most of the time biologists only looked for a long time at one gene or some more genes, at one time. In a system approach this a more (w)holistic approach is used. For example one could study the adaption to a certain environmental stress and look at transcription factors that up-regulate or down-regulate in specific conditions. Those data could be then be coupled with protein measurements, metabolites that play a role in that particular process, and more types of biological relevant data.

There are several characteristics that are important for biological network analysis. Below I summarized two of them.

  1. First of all, biological networks are neither random and have a certain design principles (which we do not know yet). From an evolution perspective that means that biological networks in diverse organisms will share common functional sub-systems. When inferring a network, one could do that based on homology, and so identify large parts of biological networks in different organisms. This would perfectly make sense in a creationist view.
  1. Second, Biological systems are modular. An inherent quality of biological systems is, that it is more likely that a set of genes performs their task as a module. So when we see an organism as a system, that means that many modules are able to perform a different task. For example you could cluster co-expressed genes which all play a role in the metal homeostasis.

What creationists could learn from biological network analysis is quite obvious. First of all, the fact that genomes are modular could be seen as a design principle. In organism A the module could behave in the same way as in organism B. Our Creator would have used modules to create everything. As a way of speaking only fine-tuning is then needed for God to ‘made the beast of the earth after its kind’ (Genesis 1:24–25).

For a creation biology model it is important to think about what homology means. It is important that creationists do not stop by just a linear view on the genome, but take in these matters a system approach, where all elements are considered.

Baraminology is the field in which a system of classification is used to identify created kinds. As is pointed out by Todd Wood (2006), the use of molecular data is kind of a  problem. Of course this problem is also known in mainstream science, when molecular data are used for tree building, that as a consequence,  trees become unreliable (for which they invented phylogenetic networks).
When I was thinking about how the systems approach could apply to baraminology I came to the following speculations. First of all, what if biological modules share homology between organisms, instead of just looking at one gene. One would expect that such a biological network module would give a more reliable estimate of similarity or dissimilarity between different baramins. The main reason for looking at morphological characters is because they give a more overall means of similarity. The hybridization criteria is used because hybridization is a ‘all-in’ character. After all for hybridization to happen between two species much of the developmental processes should be the same.

These are just theoretical speculations. For comparison of biological networks between mammals a huge amount of data is needed. And not only the genomes need to be sequenced, but also information about the regulatory of modules and of the system (organism) as a whole.

Currently, baraminology takes into account mainly morphological characters. But it would be nice, and I think everyone would agree, to also take into account molecular data. This modular homology approach could possible stimulate research into baraminology.

Any thoughts? Please let me know in the comments!

References:

Bonneau, R., 2008. Learning biological networks: from modules to dynamics. Nature Chemical Biology, Vol. 4, 11,

Wood, T.C., 2006, The Chimpanzee Genome and the Problem of Biological Similarity. Occasional papers of the BSG, 7

It’s not only poop

Today I am going to link again to a post of Todd Wood, and this time it’s about poop. His post is about research that is recently published and explains how fecal transplantation cured in 94% of the reported cases an infection with Clostridium difficile.

Todd wrote in his post that:

Creationist biologist Joe Francis, at the Master’s College in California, has long proposed that God created macro organisms (those you can see) to live in a complex partnership with microorganisms (those you can’t see).  Joe thinks that the relationships between macro and micro are essential to the health of both types of organisms, so without the proper balance of relationships, things can go really wrong.

This study provides an opening to speculation that the cause of a disease not always a question of ‘good’ and ‘bad’ germs is, but in fact depends on the balance of ‘good’ and ‘bad’ germs.

When reading his posts, my attention was drawn to several lectures that I had some time ago. In fact, I remembered that this phenomena is not only illustrated here, but that this is also observed in other organisms.

First of all I want to point out to disease-suppressive soils, which are soils where plants are protected from  particular soil-borne diseases. This protection against those soil-borne diseases occurred only in particular soils, which obviously should have properties that caused this.

Researchers found out that suppressive soils are not suppressive anymore when subjected to pasteurization (which kills all microbes). Second, they found out that suppresiveness can be transplanted (just like the poop), and that non-suppressive soils could become suppressive when 0.1%-10% of the suppressive soil was mixed with the non-suppressive soil. In short, the primary cause of the suppressiveness was caused by microorganisms. Several examples of pathogens which are suppressed by particular kinds of soils are available. Fungal pathogens such as Gaeumannomyces graminis var. tritici, fusarium oxysporum, Phytophthora cinnamoni, and many more were found to be suppressed in certain soils (Haas & Défago, 2005).

I want to emphasize that this idea (proper balance of microorganisms) was already explored at a symposium in 1963 about the ‘Ecology of soil-borne plant pathogens’ (Baker & Snyder, 1665). Researchers then thought that antagonistic microorganisms competed with pathogens, by producing antibiotics.

Further research into disease-suppresive bacteria was also done at the Wageningen university in the Netherlands, and in 2011 an article was published in Science with as goal ‘Deciphering the Rizosphere Microbiome for Disease-Suppressive Bacteria’ (Mendes et al., 2011). What was done as following: They used microarrays to identify bacterial and archaeal community members which grow in the rhizospere of the plants in disease suppressive soils and non-suppressive soils.

What they found is that in suppressive soils not the number of bacterial taxa was the key to deciphering their problem, but that in fact the abundance of those bacterial taxa relative to each other was determining whether a soil was suppressive or not.

The second example that I have is about salmon eggs, which died of a cause of a mysterious origin. And the same thing was observed, that is the imbalance of microbiota in the eggs was causing the suppression of the mysterious disease or not (unpublished).

Let’s come to a conclusion. As Todd Wood pointed out in his post:

Joe and I have long wondered if creationist insights might lead to better treatment of disease, but we were both sort of baffled about how to make microbes fight other microbes.  Well, this is how it’s done, at least for now.

And we can see that this is a widespread phenomena in plants (and more organisms).

In all these examples it is caused by the balance between good and bad.  So the fitness of an organism is in several cases related to his close neighbours and their abundance. Another question is what implications it on the long-term could have for the theory of evolution: Is actually the unit where  natural selection selects on not only the organism itself, but also includes the microbiome?

Actually, I think that Joe is going to love this post too!

sources

Haas, D. & Défago, G. (2005) Biological control of soil-borne pathogens by fluorescent pseudomonads. Nature Reviews Microbiology 3, 307-319.
Van Nood et al. (2013) Duodenal infusion of donor feces for recurrent Clostridium difficile.  NEJM DOI: 10.1056/NEJMoa1205037

Mendes, et al. (2011). Deciphering the Rhizosphere Microbiome for Disease-Suppressive BacteriaScience 27 May 2011: 332 (6033), 1097-1100. 2011 

Baker, K. F. & Snyder, W. C. (eds) Ecology of Soil-Borne Plant Pathogens: Prelude to Biological Control (Univ. of California Press, Berkeley, 1965).

Tip of the day for creationists – not re-inventing the wheel,

Todd Wood draws our attention towards an interesting letter that was published in the latest CRSQ. I quote:

A couple issues back, CRSQ published an article by Bill Johnson titled “Biogeography: a creationist perspective,” in which the author failed to cite a number of pertinent creationist writings on biogeography but nevertheless lamented that “creationists have largely remained silent on the issue.”  In general, I found the article to be poorly written, overly basic, but especially unhelpful because Johnson seemed to be unaware of what creationists had actually written on biogeography.

In the newest issue a letter from Carl Froede is published writing that many creationists have already elaborated on biogeography and that this article is not new, but overlooked a substantial amount of creationist papers about this subject.

My opinion is not really relevant, because I never published anything,  but I have seen more articles that just did not investigate already published work. 

It’s scientific misconduct and should not be done.
This is something that creationists should always remember!

My plans for blogging in 2013

Last year I started blogging in August, and since then I have published 30 posts, and when I look back several posts stand out, at least in terms of viewership. The following list is ranked on viewership and you can judge yourself whether those are also the posts with the highest score in terms of quality.

Protein evolution – Two responses
Mediocre scientists
We will be there!
There are still several games in town..
Evolutionary stasis? – Change and abruptness
Biological Similarity – Why?
Falsification, scientific theory and creationism
Facts and interpretation
Allister Mcgrath on religion
Speedy evolution and extreme fast falsification
Junk DNA revisited – Implications for creation science
Strong attitudes in a debate
Transposable Elements, Epigenetics, and Genome Evolution
Pseudogenes are indeed (sometimes) functional
ENCODE: Exciting research but little consequences
Genomics
Have a nice Christmas – last blogpost of the year 2012
Adaptive evolution or not?
Fishing and Science – an Analogy
Overview
An interesting article
Stephen Jay Gould – 10 years after his death
Are there objective research questions?
Wonders of Creation – Birds of paradise
Why open access is needed in scientific creationism
Sadly my real name is going underground
The rotten tree of life – Introduction
Focusing on the details
Why another blog about science and religion?

In particular I enjoyed blogging in general and also in 2013 I plan to publish more and more about the creation/evolution debate. It is important that the voice of the creationists is heard on the web, and I will try to do that.

What I want to do more, are posts about developments in creation science. This year in August an important conference on creationism will be held, and I expect some nice insights for creation biology from that conference.

Of course I will be blogging about what interests me and as regular readers know, this will mostly cover molecular biology and genetics, which are after all, my fields of expertise.

Second, I am planning on publish some reviews of creationist literature in several series of posts. There is one book in particular, which involves several noteworthy insights about the evolution of morale, what I want to review in the coming months.

Another point of interest is the development in the ID-community, which in my opinion is changing more rapidly than imagined, and whether that is a good development remains to be seen. Besides that, I want to examine for myself what value there is in ID-ideas for the development of creation science.

What’s more important are the developments that are going to take place in creation biology. I am thrilled to be a creationist these days, when fascinating insights about evolution and molecular genetics are published everyday. We have to learn, in order to built a biblical view on creation. We have to search for, and take up every opportunity to develop a creationist theory which explains the origin and evolution of organisms.

Finally, I sure want to wish you all the best for a prosperous, successful and blessed 2013!