Balance

Science is always working a tough room. It’s inherently progressive — we’re constantly achieving incremental improvements in our understanding, with occasional lurches forward…and sometimes sudden lurches backward, when we realize that we got something wrong. We’re performing for a crowd, the general citizenry and most importantly, the funding agencies, that expect us to fix problems and make the world better, and they’re a fickle bunch who will turn on us with disdain if we don’t keep delivering new medical therapies and tinier electronics and more spectacular robots landing on alien worlds.

Unfortunately, there are a couple of sources of tension in our act.

One problem is that we aren’t doing what everyone thinks we’re doing. The world outside the sciences thinks we’re all about making material improvements in your standard of living, or increasing our competitiveness with other countries. Wrong. We do what we do to increase our understanding. There is an applied side to science that is asking about, for instance, better treatments for cancer, but it’s built on a foundation of scientists just asking, “how do cells work?”

An analogy: imagine building race cars. Everyone watching is thinking that it’s all about winning races (that’s also the case for the backers who are paying for all the machines). But the scientists are the ones who are just thinking about what’s going on inside the engine, tracing the flow of fuel and energy, optimizing and adjusting to make it work. Put a scientist in the driver’s seat, and she wouldn’t be thinking about winning the race; if she heard a mysterious “ping!” at some point, her instinct would be to just pull over then and there and take things apart until she’d figured out what caused it. And figuring out the ping would be more satisfying than finishing the race.

So everyone criticizes the scientist for not winning any races, but the scientist is feeling triumphant because her performance wasn’t what you thought it was — she learned a little bit more about what makes the engine tick, and you should be happy about that!

So that’s one source of tension. Here’s another: funding and public support thrives on positive results, that constant reassurance that yes, we’re proceeding apace towards the finish line, but science itself thrives on criticism. Probing and patching and making fruitful errors and getting criticism that forces us to reconsider our premises and rebuild our hypotheses…that’s the progressive force behind science. And we should be appreciative when someone tells us that a major chunk of research is invalid (and as scientists, we are), but at the same time, we’re thinking that if we have to retool our labs, retrain our students, rethink everything from the ground up, as exciting as it is in a scientific sense, it’s going to be a really hard sell to NSF or NIH. The granting agencies, and the media, love the safe, reliable churn of data that looks like progress from the outside.

Which brings me to an interesting argument. On one side, John Horgan gets all cynical and critical of science, pointing out deep and fundamental flaws in peer review, the overloading of science journals with poor quality work, the lack of progress in many of our goals for science, and bemoaning the reassuring positivity of the media towards science.

…I’m struck once again by all the “breakthroughs” and “revolutions” that have failed to live up to their hype: string theory and other supposed “theories of everything,” self-organized criticality and other theories of complexity, anti-angiogenesis drugs and other potential “cures” for cancer, drugs that can make depressed patients “better than well,” “genes for” alcoholism, homosexuality, high IQ and schizophrenia.

And he’s right! We don’t have any cures for cancer or schizophrenia, and as he also points out, the scientific literature is littered with trash papers that can’t be replicated.

But on the other side, Gary Marcus says wait a minute, we really have learned a lot.

Yet some depressed patients really do respond to S.S.R.I.s. And some forms of cancer, especially when discovered early, can be cured, or even prevented altogether with vaccination. Over the course of Horgan’s career, H.I.V. has gone from being universally fatal to routinely treatable (in nations that can afford adequate drugs), while molecular biologists working in the nineteen eighties, when Horgan began writing, would be astounded both by the tools that have recently been developed, like whole-genome-sequencing, and the detail with which many molecular mechanisms are now understood: reading a biology textbook from 1983 is like reading a modern history text written before the Second World War. Then there is the tentative confirmation of the Higgs boson; the sequencing of Neanderthal DNA; the discovery of FOXP2, which is the first gene decisively tied to human language; the invention of optogenetics; and definitive proof that exoplanets exist. All of these are certifiable breakthroughs.

And he’s right!

See what I mean? It’s conflict and tension all the way through. The thing is that the two are looking at it from different perspectives. Horgan is asking, “how many races have we won?” and finds the results dispiriting. Marcus is asking “have we figured out how the engine works?” and is pleased to see that there is an amazing amount of solid information available.

Here, for example, are some data on cancer mortality over time. In this instance, we are actually looking at the science as a race: the faster that we can get all those lines down to zero, the happier we’ll all be.

Charts of cancer death rates over time

Weinberg, The Biology of Cancer

Look at the top graph first. That’s where we’re doing well: the data from stomach and colon and uterine cancer show that those diseases are killing a smaller percentage of people every year (although you can probably see that the curves are beginning to flatten out now). Science did that! Of course, it’s not just the kind of science that finds a drug that kills cancer; much of the decline in mortality precedes the era of chemotherapy and molecular biology, and can be credited to better sanitation and food handling (hooray for the FDA!), better diagnostic tools, and changes in diet and behavior. We’re winning the war on cancer!

Wait, hold on a sec, look at the bottom graph. It’s more complicated than that. Look at lung cancer; science was helpless against the malignant PR campaigns of the tobacco companies. Some cancers seem relentless and unchangeable, like pancreatic and ovarian cancer, and show only the faintest hint of improvement. Others, like breast cancer, held steady in their rate for a long time and are just now, in the last few decades, showing signs of improvement. It’s complicated, isn’t it? Horgan is right to point to the War on Cancer and say that the complex reality is masked by a lot of rah-rah hype.

But at the same time…Horgan got his journalism degree in 1983, and I got my Ph.D. in 1985. He’s on the outside looking in and seeing one thing; over that same time period, I’ve been on the inside (still mostly looking in), and I’ve seen something completely different.

If I could show my 1985 self what 2013 science publishes as routine, 1985 self would be gibbering in disbelief. Transgenic mice? Shuffling genes from one species to another? Whole genome sequencing? Online databases where, with a few strokes of the keyboard, I can do comparisons of genes in a hundred species? QTLs that allow us to map the distribution of specific alleles in whole populations? My career spans an era when it took a major effort by a whole lab group to sequence a single gene, to a period when a grad student could get a Ph.D. for completing the sequencing of a single gene, to now, when we put the DNA in a machine and push a button.

You can look at those charts above and wonder where the cure for cancer is, or you can look at all the detailed maps of signaling pathways that allows scientists to say we understand pretty well how cancer works. Do you realize that hedgehog was only discovered in 1980, and the activated human ras oncogene was only identified in 1982? It’s rather mindblowing to recognize that genes that we now know are central to the mechanisms of cancer have only emerged in the same short period that Horgan finds disappointing in the progression of science.

Everyone on the outside is missing the real performance!

Unfortunately, a growing problem is that some of the people on the inside are also increasingly focused on the end result, rather than the process, and are skewing science in unfortunate directions. There’s grant money and tenured positions on the line for getting that clear positive result published in Cell! As Horgan points out, “media hype can usually be traced back to the researchers themselves”. We’ve seen that with dismaying frequency; recently I wrote about how the ENCODE project seems to have fostered a generation of technicians posing as scientists who don’t understand the background of biology (and Larry Moran finds another case published in Science this week!). We’re at a period in the culture of science when we desperately need more criticism and less optimism, because that’s how good science thrives.

That’s going to be tricky to deliver, though, because the kind of criticism we need isn’t about whether we’re winning the race or not, or translating knowledge into material benefits or not, but whether the process of science is being led astray, and how that’s happening: by the distorting influence of big biomedical money, by deficiencies in training scientists in big picture science, or by burdensome biases of science publication, or by all of the above and many more.

But ultimately we need the right metrics and to have well-defined outcomes that we’re measuring. It doesn’t help if the NIH measure success by whether we’ve cured cancer or not, while scientists are happily laboring to understand how cell states are maintained and regulated in multicellular eukaryotic organisms. Those are different questions.

Ill-informed science making a case for a liberal arts education

Last month, I wrote about the terrible botch journalists had made of an interesting paper in which tweaking regulatory sequences called enhancers transgenically caused subtle shifts in the facial morphology of mice. The problem in the reporting was that the journalists insisted on calling this a discovery of a function for junk DNA — the paper itself said no such thing, but somehow that became the dominant message of the popular press coverage. Strange. How did that happen?

So Dan Graur wrote to the corresponding author to find out how the junk crept in. He found out. It’s because the author doesn’t understand the science. Axel Visel wrote back:

When I talk to general audiences (or journalists) about my research, I generally explain that the function of most of the non-coding portion of the genome was initially unclear and many people thought of it as “junk DNA”, but that it has become clear by now that many parts of the non-coding genome are functional – as we know from the combined findings of comparative genomics, epigenomic studies, and functional studies (such as the mouse knockouts in our paper).

Aargh. Non-coding is not and never has been a synonym for junk. We’ve known that significant bits of non-coding DNA are functional for a period longer than I’ve been alive…and I’m not a young guy anymore. The mouse knockouts in his paper were tiny changes in a few very short sequences — even if we had somehow been so confused that we though enhancer elements were junk, whittling away at such minuscule fragments of the genome weren’t going to appreciably increase the fraction that is labeled functional. That focus on finding more functionality in the genome flags Visel as yet another ENCODE acolyte.

Man, I’m feeling like ENCODE has led to a net increase in ignorance about biology.

Graur does not mince words in his assessment:

My problem is that junk DNA does not equal noncoding or nontranscribed DNA, and I am sort of sick to see junk DNA being buried, dismissed, rendered obsolete, eulogized, and killed twice a week. After all, your findings have no bearing on the vast majority of the genome, which as far as I am concerned is junk. Turning the genome into a well oiled efficient machine in which every last nucleotide has a function is the dream of every creationist and IDiot (intelligent designer), so the frequent killing of junk DNA serves no good purpose. Especially, since the evidence for function at present is at most 9% of the human genome. Why not call noncoding DNA noncoding DNA? After all, if a DNA segment has a function it is no junk.

Larry Moran is also a bit peeved, and explains that we actually know what a lot of that noncoding DNA does. It’s not a magic reservoir of hidden functionality.

I’ve said it many times but it bears repeating. A small percentage (about 1.4%) of our genome encodes proteins. There are many other interesting regions in our genome including …

  • ribosomal RNA genes
  • tRNA genes
  • genes for small RNAs (e.g spliceosome RNAs, P1 RNA, 7SL RNA, linc RNA etc.)
  • 5′ and 3′ UTRs in exons
  • centromeres
  • introns
  • telomeres
  • SARs (scaffold attachment regions)
  • origins of DNA replication
  • regulatory regions of DNA
  • transposons (SINES, noncoding regions of LINES, LTRs)
  • pseudogenes
  • defective transposons

These parts of noncoding DNA accounts for about 80% of the human genome. A lot of this noncoding DNA is functional (about 7% of the total genome [What’s in Your Genome?]). None of it is mysterious in any way. We’ve known about it for decades. As Dan Graur says, it’s a known known.

At least I’m in a position to do a little something about this ignorance. I’m teaching cell biology to our sophomores this semester, and next week I start the section on DNA replication, with transcription the week after. My students will know the meanings of all those terms and have a clear picture of genome organization.

And what that should tell all you employers out there is that you should hire UMM biology graduates, because they’ll actually have some knowledge of the science. Unlike certain people who seem to have no problem publishing in Science and Nature.

Taking zombies to task

Oh, good — both Tara Smith and Colin Purrington are a bit peeved with the recent episodes of The Walking Dead that have the survivors coming down with a nasty form of the flu, and their resident people sending them scurrying off to pillage local zombie-haunted pharmacies for…antibiotics. For shame.

They don’t mention the other things that bug me about that show, though. If the zombie plague is also viral, why aren’t they all turning into undead voracious brain eating monsters when they get splattered with zombie slime and goo and blood? They’re ripping up zombies right and left and practically bathing in disgusting fluids. Come on, people, hygiene.

Also, how long have they been wandering around Georgia? A year or two? Some of the zombies are portrayed as far advanced in decay, but others seem to be fairly fresh. Shouldn’t the zombie population be dropping off dramatically now? The pool of live humans from which new zombies could emerge is so drastically reduced that they ought to be dealing with little more than piles of ineffective rot and the very rare occasion when one of their own dies of natural causes and goes walking around hungrily.

Finally, Rick is a terrible, incompetent, awful leader. They’ve found one group of thriving humans in a town, led by a psycho tyrant — and there’s Rick’s poor struggling group who have been shredded by internal conflicts and have been succumbing steadily to attrition. The freakish violent Governor did a better job establishing a safe haven than Rick, and they destroyed it! When will the survivors learn that they’re being guided by a dangerous idiot?

Religion is destroying the nuclear family!

It’s not gays that are corrupting traditional family values, it’s god. The latest survey shows that members of Bible-believing churches are more likely to divorce than atheists are.

There are a number of explanations. Here’s one.

Secular couples tend to see both marriage and divorce as personal choices. Overall, a lower percent get married, which means that those who do may be particularly committed or well-suited to partnership. They are likely to be older if/when they do formally tie the knot. They have fewer babies, and their babies are more likely to be planned. Parenting, like other household responsibilities, is more likely to be egalitarian rather than based on the traditional model of “male headship.” Each of these factors could play a role in the divorce rate.

I also think there’s a difference between the sexes in traditional marriage, too: for women, it’s an obligation to live a life of service; for men, it’s a privilege to obtain a cheap servant who is required to give you cheap sex. That kind of differential can easily fracture what ought to be a partnership.

I’m relieved to see, though, that the article doesn’t imply that it’s something intrinsic to being an atheist, stating that it’s more like what slice of the socioeconomic pie you’re likely to get if you’re an atheist vs. a Christian, and it also suggests that the way to reduce divorce rates overall isn’t to get everyone to become an atheist, but to build a better social safety net and encourage more equality. Which also leads to more atheism, by the way, which is why the people suffering most under an unfair system will oppose changes to make it better.

I’m still going to deplore how all those religious organizations with “Family” prominently planted in their name are ironically poisoning the American family that they worship.

Halloween is for scary stories

Salon has a small collection of tiny horror stories for Halloween. The only rule is that they can only be two sentences long: so you can go for Hemingwayesque brevity or a Joycean ramble, but you’re only allotted two periods.

So I wrote one. They’re easy!

Christmastime

We had lost electricity, gas, and supplies months ago, so no sound disturbed the gentle hiss as the flakes fell, no movement marred the scene, and our houses in this sleepy little town all looked like picturesque Kinkade cottages pillowed with untrammeled snow, except that there was no curl of smoke from our chimneys, nor any ruddy glow behind the windows. Behind those dark windows rimed with ice, we all stared admiringly with hollow eyes in gaunt faces at our neighbors’ lovely homes, and with cold-numbed fingers we loaded shotguns and sharpened axes, and we thought simple, homely thoughts of wood, and fire, and warmth, and…barbecue.

Now, it’s your turn. Leave a two-sentence horror story in the comments. I’ve got a morning of teaching ahead of me, but when I get some time around noon, I’ll promote the best of them up top.

Ooh, I thought of another one!

Evanescence

Scientists had mastered immortality, but there was no way around the limitations of the human mind. By the end of the century, the world was ruled by ancient old men who had shed their oldest memories, and lacked even the faintest recollection of their mothers, their childhoods, their first kiss…

So many stories…here’s a short subjective sampling from the comments.

From texasskeptic:

Alicia was already bored, “you don’t have an PlayStation or anything?” she asked.
“I know a game we can play,” Danny said, running to his dad’s nightstand, “You can be the robber!”

From Crip Dyke:

His unfamiliar hands put down knife and fork with a bright clink that pierced me painfully even though my migraine had largely subsided, and then my date etched in my memory his admission, “Yes I’m that John Loftus, but you shouldn’t let what you’ve read concern you: I’ve learned so much lately. Have you heard of the Men’s Human Rights Movement?”

From Jonathan, der Ewige Noobe:

We stared up at it, watching the teeth dig in, the dark mass spread, rootlike, over its meal, and for a moment we imagined that we might be able to stop it.

Then someone (I can’t remember who) realized that, given the speed of light, this had happened eight and a half minutes ago.

From Rey Fox:

There are no jobs. Next, climate change.

From UnknownEric the Apostate:

Jack the MRAtheist was sitting in his hotel room, writing short misogynist screeds on Twitter, when there was a knock at the door. A voice on the other side said, “Hi, It’s Rebecca Watson.”

From dianne:

I knew it was over before I even got to the hospital: the pain was terrible and the bleeding worse, my fever was 103 but the contractions weren’t coming. The nurse came into the room beaming and said, “Great news: there’s still a heartbeat and we will treat you both with love!”

From ledasmom:

I rolled over in my husband’s arms to kiss him. I put my hand up to cradle his head and against my fingers felt the back of his face.

From miserlyoldman:

As I sit finishing reading some alarmist tripe about how a fungus like Ophiocordyceps unilateralis was in a position to turn zoonotic, driving people into open fields for spore release and some other miserable dreck that would never have the standing to be published any place respectable, I mourned the rise of clickbait journalism. I need to get away from this electronic glow for a bit, enjoy the beautiful crisp autumn air, feel a little nip in the wind in a place where I can cloudgaze for a while; it’s been forever since I’ve visited the park…

From stillacrazycanuck:

Looking down on her decaying corpse, the rotting flesh already falling from her bones, maggots crawling within her mouth and her eyes bulging from their sockets, I gave thanks that at least her pain was no more. Then she blinked.

From strangerinastrangeland:

The wiggeling mass of tentacles handed over the large bundle of dollar bills to the little boy and they shook hands – or better hand and slimy appendix of the netherworld – on their deal before it disappeared again into the darkness under the boy’s bed.

“Daddy, Daddy, there is a monster under my bed, you have to come and look and help me”, cried the boy, with a little smile on his face while counting his bounty.

Teaching is so easy, anyone can do it!

This guy, Anthony Seldon, works at a teaching school, and he has just politely dissed teachers everywhere on the pages of the Guardian.

Schoolteaching is a profession, but it’s not like becoming a doctor or a vet. No one would want to be operated on by an amateur who hadn’t had years of experience. The prospect of going to the dentist and being confronted by somebody with a lifelong passion for teeth but no university background or training would alarm all but the most steely. For that reason, there is no Teeth First, though we do have Teach First, albeit with intensive training.

Nick Clegg and others who argue that teachers must first be qualified are fundamentally misunderstanding the nature of the profession. The teacher’s role is much more akin to that of a parent. It is a great loss that governments worldwide have made teaching much less like being a parent than an impersonal civil servant. No job is more important than parenting, yet no one is suggesting parents go off for a university course to qualify as a parent. Parents pick it up as they go along, and that’s exactly the way great teachers are forged.

May I be the first to suggest, then, that maybe parents would be better for it if they actually had to prepare for the responsibilities? There are an awful lot of terrible, horrible parents out there who end up abusing children by neglect or intent.

But no, I’m a teacher, and it’s nothing like being a parent. (I’m one of those, too, so I do have rather solid grounds for a comparison.) Maybe preschoolers need a more parental nurturer, but everything beyond that…teachers are bearers of knowledge that they must communicate to their students — their diverse students who may be hostile, apathetic, or enthusiastic, who may be coming into the class unprepared or thoroughly ready, who may be disciplined or disorganized. And they damn well better understand their material.

One of the first things you learn when you start teaching is that you have to know the content inside and out — it’s simply not enough to know the bare minimum that you expect the students to master, because as a teacher, you need to push just a bit farther to get them up there. You need to be able to lead them to knowledge, and you need to be able to point off in the distance to all the cool stuff they can learn if they continue. How can you inspire if you’re not drinking deeply from the Pierian Spring yourself?

And teaching itself is a skill. It requires constant work and adjustment. In my introductory classes, I’m comfortable with the content and it requires only a little attention to keep up to date on the science, but I’m constantly fretting over how to communicate concepts better this time around. There actually is a teaching literature, you know, perhaps Mr Seldon is unaware of it. There are always new and better ways to instruct coming out and being tested, and there is academic knowledge behind it.

One of the terrible secrets of college teaching is that it fits Seldon’s ideal: most of us get almost no instruction in education as grad students, and then we’re thrown into being in charge of a class for the first time when we’re hired as faculty. And let me tell you, it sucks for both the teacher and the students. My first year was terrible. I had no idea what I was doing, I was frantically struggling to all hours of the night to figure out what the heck I’d be doing the next day, and I pity my poor students from that time.

I could dig up my evaluations from back then if I wanted a reminder of my misery. My student evaluations were bottoming out my first year; I had colleagues coming in and giving me pages and pages of advice. Those evaluations steadily rose until I had people praising me as one of the best teachers in my department…but it took five years of hard work on the job.

So Seldon compares teaching to surgeons and says, “No one would want to be operated on by an amateur who hadn’t had years of experience.” No one in their right mind would want to be taught by someone who hadn’t had years of teaching experience, either. I’d go further and say you ought to demand that your teachers be well-qualified, because you’re trusting your children to them, and they are usually only going to get one shot at learning and growing.

But Seldon thinks there is no expertise to teaching, only passion and enthusiasm.

And then there’s this.

Those who care more about themselves, are time-watchers, and place pay and conditions above caring for the young will never make it. Teaching is a vocation as well as a profession.

Do not diminish the importance of a profession standing up for self-interest. It’s true that people go into teaching because they love it, but it is entirely in the interest of the paymasters to scorn the self-respect of teachers and tell them they shouldn’t care about pay and conditions. Teaching is one of the most important professions in our society, deserving of the greatest respect, but somehow, the bureaucrats and administrators have decided that it’s not worth paying for, and that teachers who demand appropriate acknowledgment of their contributions are compromising “caring for the young.”

Nice racket. I know who’s side Seldon is on, and it isn’t the teachers’.

Double take

Elvira (Cassandra Peterson) goes for a drive with Ru Paul.

I found this on Joe. My. God., where I saw this commentary:

It’s very hard to believe that Elvira is 62.

My first thought was, yes, she looks amazing, and I was surprised that she’s that old. But immediately after I saw her birthday — 17 September 1951 — my second thought, my shocked realization, was…she’s only a few years older than I am.

Goddamn. When did that happen?

I should have Cthulhu teach my classes

Now you too can grasp the great Lovecraftian insights into biology. They’re pretty simple: you’re going to die, and the universe doesn’t care.

By the way, the article is from the makers of Call of Cthulhu: The Wasted Land, which happens to be one of only three games that I have on my iPad. It’s grim and bloody and horrible, and I’ve made it through every level except the last one, where the Leng Spiders and Cthulhoids turn my team into a rotting smear of decaying jellied flesh. Which seems fitting.

What I’d be telling my kids nowadays

I’m one of those people who is hopelessly addicted to babbling on the internet, and even I don’t understand this statistic.

the leading cause of death for teenage drivers is now texting, not drinking, with nearly a dozen teens dying each day in a texting-related car crash.

You cannot type and drive, or read and drive, at the same time. It’s really that simple. So why are people trying?