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.

Continue reading Have a nice Christmas – last blogpost of the year 2012

Advertisements

Are there objective research questions?

Scientists are often accused of presenting results not objective. But most of the time scientists try to be as objective as possible.

A better question which we could ask ourselves is whether scientists can ask objective questions? In my view scientists could answer them objective, but can they ask the questions objective?

Do you have any thoughts about that? Please leave them in the comment section!

Evolutionary stasis? – Change and abruptness

Recently I read something about species stasis and I thought that I would be nice to look into that in more detail.  First I want to define species stasis. In general  species stasis is defined as little or no morphological change in an evolutionary history, which spans several million years.

Naturally the punctuated equilibrium theory of Stephen Jay Gould comes to the mind of evolutionists. It is nowadays clear that many examples can be found that exhibit species stasis. The most well-documented examples are the Cheilostomes which show species stasis that spans 2-16 million years, without noticeable morphological change (Jackson and cheetham, 2001).

Normally it is assumed that when species display a stasis for a long period, that much of the morphological change is observed in a short time-span  in a brief time in which speciation occurs.  That’s also the core beneath the punctuated equilibrium theory of Gould (Eldredge and Gould 1972). Continue reading Evolutionary stasis? – Change and abruptness

Wonders of Creation – Birds of paradise

With thanks to Jerry Coyne for pointing out to the marvelous and miraculous pics and video that the Guardian published last week. It shows the sexual behavior of birds from the family of the Paradiseidae. 

Although my beliefs differ quite a lot from the views on life that Coyne has, we have to acknowledge that it’s indeed one of the hardest questions in evolutionary biology.

For the time being, just enjoy and wonder about why God may have created a mechanism that caused the different sexual behaviors of those birds and perhaps more important, how such mechanism would operate in nature.

 

 

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

Plagiomnium affine, Laminazellen, Rostock

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..

Continue reading Speedy evolution and extreme fast falsification

Stephen Jay Gould – 10 years after his death

During his life, a Stephen Jay Gould was one of the most prominent and known public figure who advocated evolution throughout his many books and articles that he wrote in a time span of thirty years.

His magnum opus was his book ‘The Structure of Evolutionary theory’, which is one long argument for a revised and extented form of evolutionary theory. Some critics thought indeed that it was a too long argument, and not all scientists were convinced by his arguments, but none of that matters when assessing the impact that he had on the field of evolutionary biology.

Continue reading Stephen Jay Gould – 10 years after his death

Adaptive evolution or not?

It is always fascinating to see when theoretical predictions are validated by empirical evidence. As a scientists, this is the ultimate vindication of your hard laborious work to obtain knowledge about a particular subject. And that is what is happening at this moment in evolutionary biology. In the forthcoming issue of Nature Genetics  several authors try to examine the empirical foundations of adaptive evolution.

Adaptive evolution is the process in which traits evolve by means of natural selection. In general those adaptations contribute to the fitness and survival of individual organisms. For several decades it was already known that three broad concepts underlie adaptive evolution.

  1. The probability of fixation of an allele depends on the effective population size (Ne) of the population in question
  2. The fate of the allele depends on the frequency (P0)when positive selection begins to act. So for de novo mutations initial frequencies are low and alleles are more likely to be lost
  3. The size of the beneficial effect determines how efficient selection is on a particular allele. This is called the selection coefficient

In recent decades it became more feasible and possible to analyse the signatures of selection in a genome. For example by the development of molecular techniques, like genomics,  it has become possible to quantify the amount of variation that occurs in a population for a given allele and indeed validate much predictions that were made by theoretical evolutionary biologist in recent decades.

Continue reading Adaptive evolution or not?

Facts and interpretation

the fact factory [website link]

Nothing in Biology Makes Sense except in the Light of Evolution (Theodosius Dobzhansky)

In my previous post I pointed out a striking difference in the interpretation or representation of actual data by two creation scientists. In this post I want to think this important subject in more detail.

In science there are facts, and there is interpretation, and from the first one follows the other. As humans we have to interpret the data around us to make sense of the world. When people are interpreting data, they are assigning meaning to certain abstract objects that are found to be true.

So it is an easy solution to the problem saying that creationists and evolutionists interpret fact differently, and so to say, through their different worldviews. But that’s a rather simplistic explanation for the major differences in interpretation between those two groups.

But let’s first examine the question what a scientific fact is. A scientific fact originates through application of the scientific method. And they should be independent from the one that observes that particular fact. So by now you understand that not every fact is a scientific fact. By proposing a hypothesis or theory people interpret the facts. In that way it is really clear that creationists interpret data differently than evolutionists.

And it is easy to fall into the fallacy, that every interpretation is allowed that is based on the same data. And for creationists it is easy to say that they interpret data through a different worldview and therefore stop the discussion about that interpretation.

Because there can be competing theories, which are both credible. And there can be one validated theory and another less sophisticated theory. And finally there can be one theory in which facts are interpreted by people in the same way again and again.

Is it interpreting the facts in a different way? That’s true. But at the same time it is, and will ever be, a search for the best scientific explanation of something that is happening around us. And when we cannot find another better explanation based on creation, we have to admit that evolution explains it better.

Back to the creation-evolution fact interpretation controversy. When I see how evolution makes sense of the world around us, I  really do think that evolution explains many phenomena in a better (scientific) way. Sometimes, using evolutionary assumptions it is more easy to interpret your data and to make sense of it… That is at least my experience, and I think that all creationists should admit that.

But of course, based on my ideological belief that the earth exists only 6000 years,  and that the Scripture is the key to the ultimate Truth, I have to say that I do not believe that the Darwinian conception of life is true.

But scientifically speaking I can say, unconditionally,  that the light of evolution shines very clearly over a broad range of phenomena. And my conclusion would be that interpretations in science are different from interpretations that are occurring in the daily world.

But is not a too easy answer to marginalize the role of ideology in the creation-evolution debate? That is something that I want to discuss in a future post.