Tag 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!

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!

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.

Junk DNA revisited – Implications for creation science

Junk DNA is dead. At least that is what the recent paper in Nature proposed. The press coverage was huge and responses varied. But the general reaction was that junk DNA does not exist anymore. The whole genome has a function, or at least a biochemical function.

For scientists and especially for geneticists this is a happy hour. Exciting research with exciting consequences. I was thinking about design and what implications this does have for creation science. Todd Wood said in his post about the ENCODE results that it is important that creationists do not use those results for their propaganda purposes.

And I definitively agree!

As you all know when genes are passed on through the generations, changes happen. Mutations occur. The majority of those mutations are deleterious, and could cause for example a knock-out in a gene that codes for a transporter protein that transports substances from the cytoplasm to the vacuole.

When a mutation causes malfunction of a gene, most of the times it still can be transcribed into RNA. You would expect to find biochemical activity. The functionality is gone, at least if you look to the gene product that does not work anymore. And that process happens also when you think that organisms are designed.

So you would expect DNA that does not have a real function (If you define function by having an effect on the phenotype). The number of mutations that is deleterious is huge and therefore you expect rubbish DNA that doesn’t have any impact on the growth and development of an organism. Any function does not count for real function.

And that’s why we have to look at the ENCODE results.

The ENCODE scientists have analysed 147 cell types. Each different cell type transcribes different genes and so different sorts of biochemical activity is found in different cell types. When combined they give an estimate about the amount of the genome has a biochemical activity

The authors of the article state the following:

Operationally, we define a functional element as a discrete genome segment that encodes a defined product (for example, protein or non-coding RNA) or displays a reproducible biochemical signature (for example, protein binding, or a specific chromatin structure).

And more:

From comparative genomic studies, at least 3–8% of bases are under purifying (negative) selection, indicating that these bases may potentially be functional. We previously found that 60% of mammalian evolutionarily constrained bases were annotated in the ENCODE pilot project, but also observed that many functional elements lacked evidence of constraint.

And:

Interestingly, even using the most conservative estimates, the fraction of bases likely to be involved in direct gene regulation, even though incomplete, is significantly higher than that ascribed to protein-coding exons (1.2%), raising the possibility that more information in the human genome may be important for gene regulation than for biochemical function. Many of the regulatory elements are not constrained across mammalian evolution, which so far has been one of the most reliable indications of an important biochemical event for the organism.

So when I read that, I see several things:

  1. There’s a huge amount of regulatory elements discovered in all different cell types
  2. 80% of the genome has a biochemical signature, so perhaps involved with the regulation and things like that.
  3. At least 3-8% of the bases are under purifying selection (which means that those are constrained in evolution).

But does it have big consequences for creation science? No not really. It just shows that regulation is more important and width-spread in the genome than previously thought and that probably the structure of the genome is more intricate and sophisticated than we thought. 

Evolutionary scientists have longtime assumed that when something in the genome is not constrained by selection, that it is not functional. But in the past decade more and more was discovered about the genome and the concept of junk DNA was already shrinking.

For me it was not a big surprise that much of the genome has a biochemical function. It was already known that more and more of the genome had a biochemical function. This was just the confirmation.

And it also depends on the definition of junk. What do you call a function, and what’s useless?  There are probably some implications for creation science after all. But they are little ones.

  • First of all when people ask you why a designer would fill the genome up with useless stuff, you can answer that most of the genome is functional and that this does not count as an argument against design in nature. 
  • Second you could say that it is more probably that a designer would fill up the genome with functional bases, and that the little non-functionality are remnants of our short evolutionary history, but that is a counter argument against objections to design, and not an argument for worldview based on design. 

So trivial

  • Third, The ENCODE results show that regulation is more non-constrained than the biological function that genes code for. And we know that regulation is generally more species-specific. So that could have the implications for shared ancestry, but we do not know that yet.

And that’s just speculation. We need probably an ENCODE project for apes as well (Its costs will be less than $ 1,000,000) Then we can compare it. See what the differences are and what overlap can be seen.

And we have to realize that we know less than we thought we knew. So that’s humiliating. But we cannot say that this is a major victory for ID and creation science. It’s just science progressing.

See also my previous post about the ENCODE results

Please share your thoughts!

Sadly my real name is going underground

Although I think that anonymity on the web is not promoting a fair and honest exchange of ideas, and I am inclined to say that I should make my name known to the whole world, I choose not to do that.

Since my childhood I was online and participating in various discussions and communities on the internet. The internet age has its grip on me and will never let me go.

Still, based on what I see around me on websites that promote Intelligent Design or Creation the comments are rather harsh, with of course some exceptions. I do not know what the future holds for creation science, and I do not know which path I will have to choose in my career.

Currently I am a graduate student, who aspires a get an academic career in genetics or biotechnology. Although I think that my beliefs about the origin of life and my belief in a literal version of genesis do not put constrains that career, others tend to disagree with that. It is written in the words of famous evolutionists that creationist should not aspire an academic career. The creationist movement is categorized as science deniers and are not worthy to get any scientific education.

I live in Europe. In the USA people are more open towards creationist beliefs, except on most secular universities. In the USA there is a discussion and 40% beliefs that creation is true and that evolution did not occur. In Europe people do simply agree for almost 100% with evolutionary assumptions and conclusions.

For creationists that makes it difficult to get a degree in science. I am striving to be a competent scientists as I can be, but I have to be careful with my internet presence. I do not want my career ruined because I proclaimed my beliefs and though open on the World Wide Web. Just for assurance, hereby my name is not public anymore.

I know the disadvantages, but I think that for me personally the advantages outweigh the disadvantages. When this blog still exists in the future and I know which choices I have to make for my further career I will review my decision again.

But for now I will stick to this format. Sorry for that, but sadly, I do not see any other way.