Saturday, June 5, 2010

Language!

Codgitator over at Fides Cogit Actio has recently been on a language kick, specifically discussing attempts to de-bias language and science and so on via E-Prime. Interesting stuff.

See, I happen to love analyzing language, deciphering which words evoke what kinds of ideas, etc. And since I've also been thinking about Intelligent Design as of late, I wanted to share some thoughts that combine the two subjects. This time, put briefly. More of a food for thought thing.

* Is it purely scientific to refer to a mutation as an "error"?
* Is it purely scientific to refer to parts of the genome as "junk" for any reason?

No further commentary from me for now. Just something to think about.

8 comments:

The Phantom Blogger said...

The term junk DNA is a interesting example. It is a value or judgmental term, which has become less utilized in genetics, as many of the sequences once believed to be “junk” have been discovered to have a function.

Junk DNA was thought of as a Vestigiality, a left over piece within organisms that has seemingly lost all or most of their original function in a species through evolution.

From wikipedia:

"The term is currently, however, a somewhat outdated concept, being used mainly in popular science and in a colloquial way in scientific publications, and may have slowed research into the biological functions of noncoding DNA. Several lines of evidence indicate that many "junk DNA" sequences have likely but unidentified functional activity, and other sequences may have had functions in the past."

"Still, a large amount of sequence in these genomes falls under no existing classification other than "junk". For example, one experiment removed 1% of the mouse genome with no detectable effect on the phenotype. This result suggests that the removed DNA was largely nonfunctional."

Roy John Britten through his work, showed that eukaryotic genomes have many repetitive, non-coding DNA sequences, formerly known as junk DNA, but now known to have many functional elements in organisms.

Shared sequences of apparently non-functional DNA (etc Junk DNA) are considered to be major pieces of evidence for common descent.

Some articles:

Experimental Data Force Researchers to Admit There’s “No Such Thing As Junk RNA”

The first is a link to an intelligent design website but the second is a legimate science website:

http://www.evolutionnews.org/2009/10/experimental_data_force_resear027161.html

http://www.sciencedaily.com/releases/2009/10/091013105809.htm

Intelligent Design and the Death of the "Junk-DNA" Neo-Darwinian Paradigm.

Again its a pro-ID website but it quotes from legimate souces like Wired magazine and the Washington Post.

http://www.ideacenter.org/contentmgr/showdetails.php/id/1437

Crude said...

Oh, I often follow the Junk DNA talk at Uncommon Descent and some other sites - I find that whole development interesting.

But what I'm really getting at here is what you touched on right at the start:

It is a value or judgmental term

I agree. So, what was it doing in science to begin with? For me, that function has been found for the 'junk' is really beside the point. Say no function was found. Is 'junk' still a scientific term?

I'm saying no, it's not. In fact, for all the complaints that ID is harming science by injecting unscientific views and concerns into the field, it really seems to me that if anything they are (to use a term that makes me sound like I'm 80 years old) Jonny-come-latelys.

So, back to the OP. Is it really purely scientific to refer to parts of the genome as "junk"? Is it really purely scientific to refer to mutations as "errors" (or even "mistakes")?

Not directed at you specifically, mind you. Just repeating myself.

The Phantom Blogger said...

I'm not sure that many legimate scientists would use the term Junk DNA, its used mainly by pop scientists.

There claim would be that it is just Vestigial DNA and errors, that are byproducts of the randomness of the mutations process.

Its almost like there attaching telelogical characteristics to the mistakes of evolutionary process.

Crude said...

I'm not sure that many legimate scientists would use the term Junk DNA, its used mainly by pop scientists.

See, I'm not so sure about that. Granted, the term is probably currently out of favor due to ID proponents capitalizing on it and the increased function found for the "junk". But I'll bet you I can easily find quite a lot of talk of "junk" DNA (and similar terms) in Nature, in research papers, etc.

I suppose I would say, it seems very many "legitimate" scientists are willing to become "pop" scientists at the drop of a hat.

There claim would be that it is just Vestigial DNA and errors, that are byproducts of the randomness of the mutations process.

Well, "random" is another word that has problems, without heavy qualification. It's like "unguided" in the sense relevant to ID. How is this science? What is this "error"? That's like calling Heisenberg's Uncertainty Principle a 'design flaw'. When iron rusts, is oxygen tricking iron?

Its almost like there attaching telelogical characteristics to the mistakes of evolutionary process.

Maybe, but right there: What are these 'mistakes' the evolutionary process makes? Again, speaking purely in scientific terms.

Yes, it's importing teleology. Or even importing a non-teleological view - when the science can rule on neither. I'm saying pure "science" can't tell us that anything is junk, much less that DNA makes 'errors' or 'mistakes', or that mechanisms/processes are 'unguided' in anything approaching what theists of any stripe could mean in that way.

And I think this runs tremendously deep. I've been following ID for years, and I cannot recall a single ID proponent ever stepping back and asking, "Wait a minute. Why are mutations 'errors'?"

The Phantom Blogger said...

"But I'll bet you I can easily find quite a lot of talk of "junk" DNA (and similar terms) in Nature, in research papers, etc."

From my first piece "The term is currently, however, a somewhat outdated concept, being used mainly in popular science and in a colloquial way in scientific publications"

"What are these 'mistakes' the evolutionary process makes? Again, speaking purely in scientific terms."

They would say not all random mutations are useful for us, only the ones that increase the fitness of the species are, hence they are the ones that are naturally selected. But you have to have many useless random mutations in order to find the good ones worth keeping that increase fitness. Hence the ones they haven't been selected may be "errors" or "junk" but are still there in the remnants of our DNA. When I said mistakes I meant that since evolution doesn't work through a perfect linear process just through the selection of whats good, then all the needless stuff could be referred to as mistakes or as simply useless (if the theory actually holds).

"Well, "random" is another word that has problems, without heavy qualification. It's like "unguided" in the sense relevant to ID. How is this science? What is this "error"?"

When people call a mutation random all they are saying is that it has no end goal or purpose.

"Wait a minute. Why are mutations 'errors'?"

I understand your point, we may look at a mutation and say its an error because it seems to have no function or have a negative effect such as causing disease, but through doing this we are measuring it through a prism and really asking what makes something good, hence attaching our personal beliefs and judgements about what makes something worthwhile to the specific agent or thing we are analysing, in the process we have deprived ourselves of our subjectivity and made almost a personal value judgement on a function or organism or phenomena.

We have not created any philosophical criteria for whats good and bad a-prior, if its even possible to do such a thing.

I'm not necessarily sure that through finding something with no observable function, that science can detect, and then saying that for all intensive purposes its junk, is really that unscientific, in may be bad philosophy though, the reason we attach words like "junk" to these functions is because we are looking at the data through the vale of the Theory of Evolution, and it would suggest that things with no function are just left over junk, from the thousands of random mutations that have taken place throughout the history of our genome.

The Phantom Blogger said...

All the word problems that arise when we talk about evolution seem to me to stem from the problem of using teleological words to describe a supposedly non-teleological process.

Its similar to a line from Feser's that I quoted before: if one thinks such talk is indispensible (and there is good reason to think it is) one must acknowledge that something like the Aristotelian conception of nature is correct after all.

Crude said...

TPB,

All the word problems that arise when we talk about evolution seem to me to stem from the problem of using teleological words to describe a supposedly non-teleological process.

I had a longer response to you, but it's so long it wouldn't fit in the comments section. I'll be making it a post in a moment.

My short reply here, though, is this: Whether or not a process is "teleological" is not for science to decide. I wonder if Ed would agree with this, actually. Maybe I'll ask him sometime. I seem to recall Ed in TLS viewing evolution as teleological.

My contention is that the idea that 'evolution is a non-teleological process' is a judgment science is utterly incapable of making, every bit as much as 'evolution is a teleological process'. Now, an admixture of science and philosophy, or religious belief, etc can make that judgment. But that mingling of the two is supposed to be avoided.

Science does not need to determine whether or not evolution (or much anything else) is teleological or not. We can study non-coding DNA without someone deciding 'it's junk'. And someone can still decide 'it's junk' - without needing to pretend this is science.

The Phantom Blogger said...

"I wonder if Ed would agree with this, actually. Maybe I'll ask him sometime. I seem to recall Ed in TLS viewing evolution as teleological."

Feser does believe that evolution is teleological (in your Physical Law post I made a comment quoting Feser in which he stated this) and so do I.

I know that it sounds like I am defending Darwinism and Evolution but I was really just trying to explain there own concepts.

"Whether or not a process is "teleological" is not for science to decide."

"My contention is that the idea that 'evolution is a non-teleological process' is a judgment science is utterly incapable of making, every bit as much as 'evolution is a teleological process'."

I agree with both statements.