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!

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.

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

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 Bacteria. Science 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!

Have a nice Christmas – last blogpost of the year 2012

The end of 2012 is almost there and it has been a while ago when I posted my last post. And for sure I want to wich you all wich a happy and blessed Christmas.

In this post I just want to give you the heads up of what I thought were interesting developments in science and especially in the evolutionary kind of science.

First, I want to point out to the post of Todd Wood about gene conversion as a means to get rid of ‘bad’ mutations. Recombination is the method by which cells swap parts of the genome and can get rid of bad mutations.  But it turns out that gene conversion (type of recombination) is occuring more frequently than thought. In diploid organisms gene conversion could ‘delete’ bad fragments, and copy the good ones. So be sure to check  his post about it!

One remark from my side, is that this was demonstrated in Arabidopsis, which is a plant species, and in contrary to this observation in yeast the number of crossing over events is observerd to be larger than the number of gene conversions. This diffference has probably something to do with the differences in repeat content, as the authors of the original article suggest. So the number of crossing-over is correlated with more repeats. Which indeed is logical.

Fishing and Science – an Analogy

Last week I was travelling by bus and when I had to wait at the bus station, two little boys were also waiting for the bus to arrive. Apparently  those boys had bought fishing gear and with the most proud faces I have seen, they looked at the stuff they bought and demonstrated to each other their possessions.

They were talking and really enjoying their things that they bought. When the bus arrived, they took the same bus as me, and because I was seated behind them, I could overhear their conversation about fishing and how marvelous it would be to get out on Saturday and trying to catch the biggest fish they had ever seen. They just were content with what they had bought and about what they were going to do.

Those boys marveled at the little things that life brings us. As adults, we are often more consumed with ‘bigger’ things in life. At least, that is what we do think. But the real question here is whether the biggest thing in the life of those boys is the same thing that we would aspire.

They were amazed and intrigued by simple things that happen around us. The boys were in a sense, representative of what a real scientific attitude should like.

A real scientist should be curious about what is happening around us, and should put out his fishing gear in open water and wait until a fish is caught. Sometimes big fishes are caught, but remember that most fishes are little. But many little fishes make up a big fish.

The water is open, but you do not see the fish swim. You do not know which fish you will take up. It could be a negative fish, or a positive fish. Or if you would like that, a neutral fish. For a fisherman it would be very nice to see where the fish swim, then they can trow out their fishing rod and fish up a positive result. For a scientist it is important to trow out the fishing rod blind-sighted.

Scientists should not let their feelings and ideology interfere with the results. When developing a scientific creationist theory for biological similarity, creationists should not fish out only positive results. Or more importantly, when researching evolution they should not omit all confirming results or studies. That is not called science.

We should not let that happen.

Transposable Elements, Epigenetics, and Genome Evolution

As you all know I am interested in genomics and about how things work in the genome. And more importantly, in the diversification process that happened after God created the earth and subsequent diversification which happened after the devastating Flood.

One of the explanations is that transposable elements have played a big role in genome evolution and perhaps they can be the cause of the enormous diversification of species that we see in nature.

In the academic journal Science, in November an article was published that illustrates the profound impact that those little, but abundant genetic elements have on genome evolution. The author of the article said:

"It is becoming increasingly difficult to escape the conclusion that eukaryotic genome evolution is driven from within not just by the gentle breeze of the genetic mechanisms that replicate and repair DNA, but by the stronger winds (with perhaps occasional gale-force gusts) of transposon activity. The ability to evoke rapid genome restructuring is at the heart of eukaryotic evolvability—the capacity of organisms with larger and larger genomes to maintain evolutionary flexibility."

In fact, that’s what evolutionistJames Shapiro, and others have been saying for years. It is nice to see that science finally progresses towards a more accurate view of evolution.

But in the light of these findings and confirmations, it is becoming more and more interesting to be a young-earth creationist these days!

Speedy evolution and extreme fast falsification

Often creationists try to show that predictions of evolution don’t come true and in most cases they state that it fits perfectly well with a creationist perspective. When reality finally sinks down in the brain of creationists they will acknowledge that it is not thát easy..