Category Archives: science

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!

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!

Protein evolution – Two responses

Recently an article was published about protein evolution in the prestigious journal Nature. It showed that a combination of two mutations is enough to switch the binding specificity of  that particular protein to another class of binding ligands.

For this study, McLaughlin et al. used a small peptide and mutated every amino acid in this peptide to create 1578 variants of the original protein. All those proteins were checked for binding to the normal binding partner of this protein (PSD95pdz3). The results are that substitutions on 75% of the sites did not have any influence on protein function, but they showed that two coordinated mutations are needed to effectively change the binding partner of this protein. In fact, they showed that although two muations are needed, that there was also an intermediate, which did bind to both binding partners.

Mutational gain or loss of function at each position of protein relative to wild type protein (red:gain;blue:loss;) Taken from McLaughlin et al. 2012

The implications of this study are profound for the way we thought that proteins evolve. It confirms the prediction that most of the mutations have little effect on a protein and proteins are in fact really resilient to change.

The Intelligent Design community claims that mutations are really bad for someone, and that proteins are ruined most of the time when a mutation occurs. But this study shows that – although for one protein – this is not the case. Furthermore this shows that proteins in theory can evolve a new function, which is in absolute disagreement with the predictions of Intelligent Design. Creationist Todd Wood already pointed this out several weeks ago on his blog.

But he also pointed out the implications for creation science. His conclusion was the following:

As for me, I’ve always thought that the resilience of proteins to mutations spoke well of their original design.  Proteins are not incredibly sensitive to mutation, breaking down the minute one mutation happened.  That would be a terrible design.  Instead, they’re built to last, which is what I would expect from a wise designer.

And I agree completely with that!

But of course not everybody. An article that was written by Dr. Tompkins at the ICR  disagrees. In fact, they think that this study shows that protein cannot really evolve new functions. What they say is the following:

Data from similar, but less extensive, studies prior to this one show that random mutations in even the simplest of bacterial proteins have impossible hurdles to overcome if they are to create new function, even if it only happens one amino acid at a time. It also showed how key sectors of proteins are so tightly designed that they tolerate virtually no change whatsoever.

If you read the study of McLaughlin carefully you will immediately see that they say that proteins are sensitive to mutations in particular regions and that proteins are also insensitive in other regions. At the ICR they see this as a confirmation that proteins cannot evolve.

The article states that most of the amino acid positions the protein is not sensitive to mutations. They show that only 20 out of 83 amino acids do not tolerate mutations.

Most positions show little effect on mutation, tolerating nearly every substitution even if radically different in chemical character (Fig. 2a–c and Supplementary Fig. 5). This  includes some that are in direct contact with peptide ligand (for example, 326 and 380), and some that are buried in the protein core and largely conserved (for example, 314, 316, 356, 357 and 390). By contrast, a subset of positions (20 out of 83, Fig. 2c) shows significant sensitivity to mutation (.2s from mean). Within the binding pocket, His 372 tolerates essentially no other substitution and Leu 323, Phe 325, Ile 327, and Leu 379 show tolerance to only the most chemically conservative mutations

That gives some credit to the claim that they make at the ICR. But they forget to mention that they also did a mutational study in which they changed the binding partner of the protein to another. Only two coordinated mutations are needed. And moreover, they show that they found an intermediate that has binding affinity for both binding partners. That means new function (or change in function)

At the ICR they cite Douglas Axe, who showed that amino acids that are used to make binding site for a protein, and thus have a direct influence on function, are extremely sensitive to mutation. That’s true, but this study shows that  protein evolution could happen.

Unfortunately for evolutionary concepts, these sectors are exactly where nature would need mutations to occur in order for it to construct new cellular interactions that might contribute to a new, selectable trait.

Wait a moment! If evolution should have a mutation in these sectors, why did they found a protein that has an intermediate binding specificity and a protein in which the binding partners were switched? I would call that an example of protein evolution in action. 

Imagine if this sort of experiment was done in more complex proteins that are hundreds of amino acids in length, or protein complexes that also include metal ions, carbohydrates, and ribo-nucleotides integrated into their structures.

And why should that be else for other (bigger) proteins. We know that substitutions are most of the time neutral? Or nearly neutral. But this finding is more likely holding up for bigger proteins.

It is interesting to view the interpretation of two young-earth creationists. But what shame is there for creationist to admit that God created a robust creation, which precisely is in accordance with the view that mutations are not always ruining protein function? Also the respons from the ICR shows that they are heavily influenced by the intelligent design movement, and it remains to be seen whether that is the right track…

McLaughlin et al. 2012. The spatial architecture of protein function and adaptationNature10.1038/nature11500 

Any thoughts?

We will be there!

The future of creationism relies for the larger part on the next generation of creation scientists. No one would disagree with that. The Next Generation of Henry Morris, Wood and others has not yet risen. At least that is what the Natural Historian said on his blog in an article with title ‘The Next Generation of Creation Scientists‘.

Simply said the post is about why and how a young earth creation scientist is generated.  Education indoctrination is one, and that does not create scientists. Many creationist call themselves scientists, but they aren’t.

Scientists are people who strive to understand the (natural) world based on observations. To make sense of the world in a scientific way, one needs to be educated in.. yes.. science.

That’s important. Young Earth Creationists need to be challenged. When I am following classes about evolution and genetics, I constantly hear that the earth is created billions of years ago. The organisms have evolved from simple to more complex as man.

And it takes a considerable amount of energy to keep up with that. It’s not easy. It is not easy to attack well-known principles in evolutionary theory. But there are people who are trying to be good creation scientists and they can do that.

And when good scientists are formed, and the keep faith, they will become good creation scientists. But you’ve got to have strength. And you have to come up with the willpower to think critical. But the bottom-line is that this is not enough.

When I graduate I hope to continue my career in science, but at the same time I hope to   have my own family. And to become a good creation scientist you need to invest a lot of time and energy. And than the question is what are your priorities.

But there will be creation scientists in the future. Just watch. And they will built upon the foundations that Henry Morris and colleagues have placed firmly on the rock that is the Bible.

So there will always be creation scientists. I want to be one. And I know several other students in genetics who are willing to contribute to a creationist worldview.

And the key to get more creation scientists, is to heavily invest in science education. And be open as a community to criticism.

Allister Mcgrath on religion

The Dutch organisation ForumC recently had an interview with Alister McGrath about his faith. He explains that he was in his youth a very aggressive atheist, partly because the religious tensions that were happening around that time in the world.

His  conversion to religion happened when he was studying chemistry at the university of Oxford. In the interview he states that a deeper knowledge of the philosophy of science caused him to think that atheism did not have ‘the intellectual resilience’ he thought it has in his youth.

I embedded the video below. See for yourself (some words are in dutch, but the overall meaning is clear).

Pseudogenes are indeed (sometimes) functional

Pseudogenes are sequences that originate from functional genes, but are not coding for proteins. Originally it was thought that pseudogenes were non-functional and that they were artifacts from the evolutionary history.

But recent developments in science propose another theory that is radically different.

The origen of pseudogenes can be explained by the retrotransposition of functional mRNA that is randomly inserted in the genome. They are similar to functional genes, but lack introns and other characteristics. A second mechanism by which pseudogenes could originate from duplicated genes that have accumulated deleterious mutations and therefore are not functional anymore.
Pseudogenes are abundant in all eukaryotic organism and in in humans 12,000 pseudogenes show evidence of being pseudogenes. A remarkable insight is that 60% of the pseudogenes in humans are also conserved.

..The high abundance and conservation of the pseudogenes in a variety of species indicate that  selective pressures preserve these genetic elements, and suggest that they may indeed perform important biological functions..

Recent evidence has demonstrated that more and more of the pseudogenes are transcribed in various organisms. The authors of the article conclude that:

..that the pseudogene transcripts are in fact functional but not random products. More and more accumulating examples support this alternative explanation..

The overall conclusion of the article is that:

..The study of functional pseudogenes is just at the beginning. There remain many questions to be addressed, such as the regulatory elements controlling the cell or tissue specific expression of pseudogenes. But, definitely, the so-called pseudogenes are really functional, not to be considered any more as just “junk” or “fossil” DNA. Surely, many functional pseudogenes and novel regulatory mechanisms remain to be discovered and explored in diverse organisms…

One of the major implications of this discovery is that the portion of junk DNA in the genome is steadily shrinking. Evolutionary theory says that pseudogenes are random byproducts of evolution in action. But this demonstrates that the portion of the genome that is non-functional is less than expected.

Scientist discover over and over that most of the genome is functional,  that genomic structures are more complex than expected and that non-coding DNA has a remarkable impact on regulation of essential biological functions. To me, it seems therefore more justified to say that this gives more credibility to the concept of a designer.

Mediocre scientists

The famous Darwinist Jerry Coyne refers on his blog to

English: Orange Ichneumonid wasp, possibly Net...
Orange Ichneumonid wasp, possibly Netelia ephippiata. Parasitic wasps, laying their eggs in the larvae of Noctuid caterpillars (Photo credit: Wikipedia)

an episode of The Life Scientific, which is a series of interviews done with leading scientists by the BBC radio.

Yesterday another installment did air and it can be viewed here. It featured Steve Jones a Welsh geneticist. The episode is quite interesting because he talks about how he got into science and also about his current research.

One little remark of Steve Jones caught my attention. He says that ‘Science is the refuge of the mediocre’. He said this because all scientists and even the mediocre ones will ultimately add some knowledge to the immense pile of knowledge that lies around. In contrary to art or music, the achievements of ‘mediocre’ scientists always count. This is really a unique perspective on science for me.

It is a fact that most mediocre scientists do add some knowledge, but mediocre scientists can also be of great danger to the quality of science.

Last year I attended a seminar on the evolution of parasitic wasps. The scientist presenting his research had thought of some very sophisticated hypothesis to explain the co-evolution of parasitic wasps and their hosts.

Much of the critique that was made in the discussion afterwards was concerned with the models he developed. The models that explained the evolution of the wasps and predation were very intricate, but the results could be explained by a simpler mechanism.

From what I understood (I am not an entomologist so let’s be clear that I am not an authority in this field) this simpler mechanism had been used in various other example of the co-evolution of wasps and their hosts. This illustrates the danger that lies in mediocre scientists. Bad science done by mediocre scientists has caused to many problems. We all know the examples.

And there really should be no problem when such scientists are functioning in a sound scientific climate. In a proper academic climate such errors in scientific thinking will be eliminated. But that is certainly not the case in all universities and institutes.

But what if it just goes in the huge mountain of knowledge? It will stay there and that will cause confusion among the better and excellent scientists..