Field of Science

Uncommondescent Unfockinghappy Unfockingfortunately

Uncommondescent makes Jesus facepalm
About a week or so ago, I noticed a spike in traffic to a post I wrote. The post was about how I see science being written and disseminated more and more from a PR standpoint. It's more about selling your work as totes-magotes awesomeness, about claiming no one ever once could have possibly grasped the revolutionary new paradigm you figured out, about how your one result is changing how we think about cell biology, cancer, the world, nay the fucking universe. That kind of crap.

Apparently this is how 'science' is done in the intelligent design creationism community, so the people at uncommondescent took offense. I utterly love the title:
Precious: American atheist finds ENCODE to be bullshot science
My post was many things, but I didn't consider it to be precious. Regardless, thanks!

I am American and my post was specifically how I see science changing in the USA (you can tell from my title, where I use the acronym USA), so it seems relevant that uncommondescent would note my nationality.

I am an atheist, and proud to state that. How that relates to my post on how I perceive science is being sold seems irrelevant. I also have black hair, albeit with some gray, why not title the post: Precious: Graying American finds ENCODE to be bullshot science. I am a parent so maybe: Precious: American dad finds ENCODE to be bullshot science. I'm also a scientist, which seems relevant. It's more relevant to my post than my views on god, my hair color, or parental status. But you know what, me being a scientist is not relevant to uncommondescent's post. In fact, I'ld argue it undercuts the strength of their post. Pointing out I think their god is hooey, is essentially poisoning the well so that their readers, conservative christians, will not bother reading my post or thinking. (I was going to write more after 'or thinking,' but realized I didn't need to.)

Also, I used the word bullshit, not bullshot. Bullshot makes no sense. What the fuck is bullshot science? Unless you're an 8 year old and think jesome crow or freaking or shoot or darn does not mean exactly what everyone knows it means. As an adult I will say Jesus fucking Christ shit damn. Not all the time, but when I think it is appropriate. If someone writes something I want to comment on or acknowledge, I will not change their word because I am too delicate to deal with it.

Here is their beef with my post:
Not exactly the way he pronounced it, but read it  here. Readers will remember that ENCODE found that, contrary to Darwinian (Christian or otherwise) hopes, there was very little human “junk DNA” — and those people have been having a fit about it ever since:
Note, they link to my post (thanks), but won't someone think of the children! I used adult language in my post and they just willy nilly put in a link to it without considering the ramifications of a reader seeing words like bullshit! But let's get to the meat of their argument: ENCODE found that little human DNA is junk and that this finding is contrary to evolutionary science. Two questions:

1. Did ENCODE find that little of the human genome is junk? No. The ENCODE authors changed the definition of 'function' as it is generally used in genome biology and then used their definition to claim that most of the human genome does something. It's true that all of the genome does something, every last base does something, 100% of the genome does something. Each base is bound by DNA polymerase and used as a template to make a copy of the cognate strand. This stuff was suggested by Watson and Crick in 1953 and demonstrated shortly thereafter. But this is 'trivial' function and not what 99.9999% of scientists mean when they discuss genome function, at least until ENCODE. Regardless, the issue is not how we use the word function, it is whether having a function promotes a piece of DNA from junk to non-junk status. In my car I have some old receipts for gas on the floor. It's there, I can show it does something, like absorb water from my wet boots when I get in the car. As far as the car is concerned, it's still fucking junk.

2. Is junk DNA a prediction of evolutionary biology? No. In fact, we've known about the E. coli genome for almost two decades and understood much about it before we had the entire sequence. Know what? It almost all does something, there is very little junk in there. I would love to see some publications that support the idea that junk DNA is required in evolutionary theory. And please for fuck's sake don't use the term Darwinian evolution when discussing junk DNA. DNA was not even known to be the genetic material when Darwinian evolution was developed. Avery, McCarty, and MacCloud published the definitive work in 1944 (Origin of Species came out in 1859). Hell, the Modern Synthesis had been well established by the time DNA was linked to heredity.

Now I'll admit there may very well be papers out there suggesting that junk DNA is required for evolutionary theory to be tenable. The point is not only to find support for your position, but to deal with the contradictory evidence and ideas as well. This was part of the point of my original post.
These issues are what concern me most. This is not how I was trained as a scientist and is philosophically opposed to my understanding of the scientific process. In science, at least at the core, we try to prove ourselves wrong. We do not try to prove that X causes Y, we try to prove that X does not cause Y. When we obtain data that undercuts a paradigm, we do not write a fucking press release, we first consider how we fucked up the damn experiment! 
I mean unless you work for ENCODE, then fuck it.
Notice, he chooses ENCODE (“if ENCODE is right, then Evolution is wrong” to rant about).
Upon reading the above sentence from uncommondescent, does anyone think it suggests I wrote 'if ENCODE is right, then Evolution is wrong'? Because that line comes another intelligent design creationist (who also has issues with big kid words).

What amazes me is that I used ENCODE as an example of what I perceive is the problem exactly one time (in a 778 word post). I also mentioned the paradigm shifting rewriting the textbook work on arsenic bacteria. I was also going to use the Darwinius masillae fossil with it's joint publication-TV special clusterfuck but I couldn't remember the name off the top of my head when I wrote the post. None of this shows up in their response. In fact, the entire point of my post was ignored, it's almost like they had an agenda and simply jammed my post into their framework. If it makes you feel better uncommondescenters, I put an update in my original post just for you.

The Changing Climate of Science in the USA (not a post on climate change)

UPDATE: If you are coming from please substitute the letter o for all letter u's to avoid 'the vapors'. Also, substitute Darwinius masillae anytime you see the word ENCODE so you won't miss the fucking point (to make things easy, you'll only have to make this substitution once).

One of my heroes: from here
I have seen a shift in the way science is being conducted in the United States. This shift still reflects of minority of the science being done, but it also represents the majority of the science being reported or disseminated to the public. In short, it appears to me that the pendulum has swung from favoring rigorous science to favoring and rewarding what I will call 'splash' science. To be clear this struggle between rigorous and splash science is not new nor different than in previous generations. Nor is all rigorous science not splash and vice versa. However, I think in the US the pendulum has swung dramatically to the splash at the expense of the rigorous. This change in trajectory is not surprising as funding has constricted immediately following a massive expansion. There are too many mouths at the trough and they are competing for those few morsels of grain.

More and more, scientific research is being sold on its revolutionary impact and not on its scientific merit. Of course 'impact' sounds much more important than 'merit'. Hell, important and impact both begin with the letter 'i' so there must be something to that. It seems much more science is being sold as 'paradigm shifting,' 'completely unexpected,' 'novel' (the only one that is true, but only in the trivial sense), or 'needing to rewrite the textbooks.' In these cases, it's also 99.99999999% bullshit (e.g. ENCODE).

2nd edition, 2011
Now admittedly and importantly, there are many studies that reveal unexpected results that lead to interesting and a variety of unexpected questions, which can themselves lead to new insights. For example, I sat in the audience at an American Society of Microbiology conference on Candida and Candidiasis where the phenomenon of white-opaque switching (a well known but poorly understood phenotype of certain Candida albicans strains) was directly and elegantly linked to mating (a process that, at the time, had recently been described but the biology nor the relevance was not understood). This was one of those 'HOLY SHIT!' moments that was amazingly cool, but also neither paradigm shifting nor required the rewriting of textbooks. In almost every single case these types of studies will not shift a paradigm nor require the revision of any textbooks. The results may be unexpected, but at most they will lead to the addition or significant revision of chapters in specialized topic books, such as the Candida and Candidiasis book from ASM.

It could be argued that inflating the importance of a study does not undercut the underlying data. But this argument is generally wrong at several levels. First, in order to emphasize the ephemeral, the actual suffers. In order to emphasize the ability to grow in high levels of arsenic, Wolfe-Simon focused on the bacteria using As in place of P in DNA and other macromolecules. The ability of the isolated bacterium to grow in such high concentrations of arsenic is interesting, but this was ignored to focus on the rewriting of textbooks on the structure of nucleic acids, which was wrong. Second, to push your paradigm shifting results, you have to actively ignore or overlook the contradictory data, even that data contained within your own work. Third, you have to discount and/or disregard the data, usually mountains of data, that led to the current paradigm in the first place.

These issues are what concern me most. This is not how I was trained as a scientist and is philosophically opposed to my understanding of the scientific process. In science, at least at the core, we try to prove ourselves wrong. We do not try to prove that X causes Y, we try to prove that X does not cause Y. When we obtain data that undercuts a paradigm, we do not write a fucking press release, we first consider how we fucked up the damn experiment! We do not identify the next great anti-cancer therapeutic target, we identify a protein that is required for uncontrolled cellular replication in a certain cell line under certain growth conditions in the lab.

If we as scientists, have truly identified a paradigm shifting result or established that the textbooks need to be rewritten, this will come out in the end. If we hoist ourselves by our own petard, then we have a problem. Think about this, when we push these boundaries of science as I see happening too often in publications and manuscripts I review, are we any different than the snake oil salesmen of yesteryear, or the person at the other end of the psychic hotline, or the politician that assess every problem to some simplistic social issue we already agree with.

We're scientists. We're better than this.