Weird Word of the Week: Stochastic

The word "stochastic" is thrown around so much in the articles about the supposedly new research finding that chance mistakes in DNA replication are the cause of many cancers that I thought I'd look it up.

Here's the first definition that appeared when I Googled "stochastic": 

adjective: stochastic: randomly determined; having a random probability distribution or pattern that may be analyzed statistically but may not be predicted precisely.

According to Wikipedia, "In probability theory, a purely stochastic system is one whose state is non-deterministic (i.e., "random") so that the subsequent state of the system is determined probabilistically. Any system or process that must be analyzed using probability theory is stochastic at least in part.^[1][2] Stochastic systems and processes play a fundamental role in mathematical models of phenomena in many fields of science, engineering, and economics.
Stochastic comes from the Greek word στόχος, which means "aim". It also denotes a target stick; the pattern of arrows around a target stick stuck in a hillside is representative of what is stochastic.

 In other words, "stochastic" means "random." Here's an image used to illustrate a course called "Stochastic Processes," taught in the Electrical and Computer Engineering Department at Utah State University in 2006. 

Course description: This course provides an introduction to stochastic processes in communications, signal processing, digital and computer systems, and control. Topics include continuous and discrete random processes, correlation and power spectral density, optimal filtering, Markov chains, and queuing theory.

Another image that could illustrate "stochastic" might be the pattern of clothes thrown in the general direction of the dirty clothes hamper when my home was occupied by several people with not the greatest aim. 

Unfortunately, I can't find a photo of that on the Inter Web. However, I just made my very own photo of that, with my very own pile of socks and my very own dirty clothes hamper:

Stochastic scattering of socks thrown in the general direction of the hamper (Or is this a better illustration of entropy?)

Bad Luck Vs. Cancer --- Or, Research Vs. Bad Science Writing

--- Or, How to Get Your Research Published

Pancreatic cancer cells dividing. Random mutations in DNA are behind two thirds of adult cancers, a study says. Photograph: Visuals Unlimited, Inc./Dr. Stan/Getty Images/Visuals Unlimited (I love this photo because it has approximately nothing whatsoever to do with the article! But photos like this accompany many articles even though they don't illustrate anything reported in the article.)

The front-page, right-upper-corner headline in my local newspaper last Saturday (January 2, 2015) was "Cancer often just random bad luck." I immediately figured this statement was wrong. Many studies have shown that behavior (e.g., smoking), environment (e.g., sun exposure), and genetics (e.g., kidney cancer and some breast cancers) can all affect a person's chances of getting cancer. So I assumed this was some ill-informed science writer who had gotten the details wrong. I was wrong about that, though.

Apparent digression which however will turn out to be important to the rest of this post:

Last semester I sat in on a graduate-level entomology seminar which focused not only on biological methods of controlling pests but also on what makes research papers more attractive to, and therefore more likely to published in, major scholarly journals.

With each of the four articles we discussed each session, we talked about the issues the authors addressed (such as the harmful effects of many pesticides, the effectiveness of biological controls, possible good or bad effects of combining  the two methods); as well as the experimental design, conclusions, flaws in the study, and how similar research might be done in the future.

See how I've inserted this photo here? "The seven-spot ladybird is a species of beetle belonging to the family Coccinellidae. It is used in biological control, of aphids in particular." I just want to put in some pretty pictures so people won't get bored with all the text that follows! And at least this one has something to do with biological control.

We also discussed how the researchers had pitched their work to the journal editors. (We didn't use the word "pitched," but that's what we were talking about.)

Because it is possible to do some ground-breaking research in the field of farming (puns intended) without anyone's noticing, if you don't get your work published; and you won't get your work published unless it's obvious early in the editorial/publishing process that your article will make the journal look good.

I bring this up  because it turns out that the science reporter in this case did not get it wrong. Instead, the authors of the study made a very effective pitch to Science, the scientific journal in which it was published.

Not only that, but the publicity people at Johns Hopkins, where authors Cristian Tomasetti and Bert Vogelstein performed their research, made an even more effective pitch to the public via the media.

Because here's the thing: Even though the study does not report ANY NEW RESULTS whatsoever. many science and medical writers came up with those headlines about "random bad luck" directly from the subject line of  the Johns Hopkins news release, "Bad Luck of Random Mutations Plays Predominant Role in Cancer, Study Shows." Here's part of that news release:

"Some tissue types give rise to human cancers millions of times more often than other tissue types. Although this has been recognized for more than a century, it has never been explained. Here, we show that the lifetime risk of cancers of many different types is strongly correlated (0.81) with the total number of divisions of the normal self-renewing cells maintaining that tissue’s homeostasis. These results suggest that only a third of the variation in cancer risk among tissues is attributable to environmental factors or inherited predispositions. The majority is due to “bad luck,” that is, random mutations arising during DNA replication in normal, noncancerous stem cells. This is important not only for understanding the disease but also for designing strategies to limit the mortality it causes."

In other words, "random mutations" during DNA replication cause cancer in cells that were normal before replication, and this happens in more than two-thirds of the cancers this research team studied. Wait! We already knew that, didn't we? Yes, we did!

From an Evolution 101 class at U.C. Berkeley, but we've all seen illustrations like this in high-school textbooks, haven't we?

From the body of the article, which I cannot access(*) but which science writer David Gorski accessed and quoted in his analysis of the article:

In formal terms, our analyses show only that there is some stochastic factor related to stem cell division that seems to play a major role in cancer risk. This situation is analogous to that of the classic studies of Nordling and of Armitage and Doll (10, 29). These investigators showed that the relationship between age and the incidence of cancer was exponential, suggesting that many cellular changes, or stages, were required for carcinogenesis. On the basis of research since that time, these events are now interpreted as somatic mutations. Similarly, we interpret the stochastic factor underlying the importance of stem cell divisions to be somatic mutations. This interpretation is buttressed by the large number of somatic mutations known to exist in cancer cells (14–16, 30).

Gorski comments, "In other words, even if taken at face value as reported in the media, Tomasetti and Vogelstein haven’t really demonstrated anything new. We’ve known for a long time that there is a strong stochastic (probabilistic) component to cancer development" (my emphasis).

Here's a figure from the paper itself, again, not accessible by me (or you, most likely), but accessed by writers Bob O'Hara and GrrlScientist** at The Guardian. They title the piece, "Bad luck, bad journalism, and cancer."

 They write, "These data suggest there is a relationship between risk of cancer and number of cell divisions. But it says nothing about the proportion of cancers due to cell division.
They continue, "So where did this two-thirds ratio come from? It is the proportion of variation in the log of the cancer risk that can be explained by cell divisions. But this variation could be the same regardless of whether the baseline risk is high or low. For example, the depth of the water in the Marianas Trench goes up and down with the position of the moon, so this explains a bit of the variation in its depth. But that reveals bugger all about the absolute depth of the trench" (again, the emphasis is mine).

And, they add, again using figures from the paper: 

"We can see this visually below: in the two data sets, x explains just under 80 percent of the variation. In the black points, x explains more about the absolute risk rates (about 75 percent). But it explains less in the red points (which is about 30 percent, as it happens) because there is much more risk (i.e. more cases of cancer) when x is zero (i.e. it has no effect). So adding some cases to that baseline only increases the total risk by a small percentage. 

"So, what proportion of cancers are due to bad luck? Unfortunately it’s difficult to tell from the paper. The figure from the paper is on the log scale, and if we extrapolate the model to zero (no cell divisions), we’d see it assumes there is no risk of cancer."

They point out another flaw in the title/headline for the paper:

"How could we decide how much of the cancer risk is due to bad luck? Well, first, we have to decide what is bad luck, which is an entirely different argument. But after we’ve done that, the only real way to suss out how much of the cancer risk is due to bad luck this is to either estimate the rates at which people get cancer through bad luck, or (perhaps easier) to estimate the non-bad luck rates" (yes, again, my emphasis).

Another analyst, Andrew Maynard, concluded that it wasn't the science writers but the authors themselves, and the Johns Hopkins publicists, who reported the story wrong:

"In the case of this paper, it’s hard to see clear evidence of bad reporting.  There is a lack of balance and contextualization though that, it seems, has its roots in the original paper" (my emphasis).

Maynard goes on to say that he's not criticizing the paper, but asks, "...how can we encourage exploratory risk research without it prematurely impacting consumer and regulatory decisions?”

And I would ask this question, which I think is more important: How can we encourage researchers and research journals to be more honest, even if less headline-producing, in their reporting of research results?(***)

(*I will be writing more about this --- accessibility of articles from science, medical, and other research journals --- in the future.)

(**Check out the blog of grrlscientist. I especially enjoyed reading her review of science books published in 2014.)

(***I will be writing more about this, too --- the reliability, or unreliability, of published research results --- in the future.)

Bad Religion Vs. Bad Science

Nobody is going to win this battle!

I've been appalled lately when reading posts on evolutionists' Web sites. The problem I've been seeing with them is that they aren't content to discuss why Darwin's theory of evolution is "true" but seem intent on blasting creationists' beliefs.

The problem with that is that this is an argument nobody will win, and everybody will lose. The creationists will dig in their feet even deeper, refusing (understandably) to consider ideas that are presented as vile-tasting medicine; which will cause even more dislike and misunderstanding of the concept of evolution,  which will further pit parents against teachers, voters against legislators, and science itself against religious belief.

And the problem with that is that nobody on either side will work toward clarifying the nature of belief and faith; nor the nature of scientific evidence and what can be proven and what cannot be.

What is "bad" about this kind of religion and this kind of science is that no one seems willing to acknowledge that both approaches seek the same end: understanding of the world, our existence as humans, and human moral imperatives.

Articles with titles like "God is on the ropes" may certainly win readers, but they don't really have anything (except vaguely derogatory generalities) to say about God or the people who believe in God.

Talk about setting up a straw man so you can set fire to him! The problem with this approach is, of course, the stench of the ashes that remain, when believers and non-believers alike walk away from the flames that had transfixed them, and attempt to look at the real issues. In the case of this article, the stinking ashes come about three-quarters of the way through, when the author admits that the theory he has been lighting up the sky with is still just a theory and has not been proven (and does not address the issue of whether this theory can be substantiated).

And the concluding paragraph is stunning in its arrogant hypocrisy and self-satisfied back-patting. No wonder creationists have sometimes "paint[ed] scientists as arrogant..." Here it is:

"Creationists often cast themselves as humble servants of God, and paint scientists as arrogant, know-it-all rebels against him. But, unsurprisingly, they’ve got it all backwards, once again. England’s work reminds us that it’s scientists’ willingness to admit our own ignorance and confront it head on — rather than papering over it — that unlocks the great storehouse of wonders we live in and gives us our most challenging, satisfying quests."

Really? In what way has this article shown any lack of arrogance? In what way has it been about "willingness to admit...ignorance"? In what way is it about a "challenging" or "satisfying" quest? Just turn this statement around for an equivalent example of what a creationist might write about evolutionist ideas. But why bother? There's enough of this kind of nonsense on both sides already. I bring up this latest example only to show the shallowness, insincerity, and mean-spiritedness of this entire debate.

What I'd like to see on the side of evolutionists is new ideas presented as new ideas, without the extra fire-starting materials. On the side of creationists, I'd like to see an understanding of Darwinism instead of a series of misunderstandings and arguments that misrepresent the theory of evolution.

Most of all, I'd like to see what true religion and true science have to say about the issues that we are all struggling with, the "great storehouse of wonders we live in," the purposes and meaning of life.

I'd like to see scientists and religious people focus their energies on solving world hunger, disease, and wars.

And I'd like to point out that for many scientists, their religious beliefs do not conflict with their scientific studies, and their scientific research does not contradict their religious beliefs.

And that's because they are interested in true religion (from the Latin re+ligare, or re-connect) and true science (from the Latin scientia, or knowledge).

(I'll be writing more about this.)

Dermatology at KP Northwest

As a person who has survived skin cancer (malignant melanoma), I've been told by my so-called primary care physician as well as every dermatologist I've ever seen at various Kaiser offices in the Portland-Vancouver area, that I should have a skin check once a year.

So when I called the Kaiser appointment desk a few weeks ago to make an appointment to see a dermatologist, I was surprised to be told that I couldn't.

Why? I wondered. Because they don't have any dermatologists in my area any more, I was told. So I could drive more than an hour to one of two remote locations where they do have a dermatologist. Or I could wait until my "turn" came up on the long waiting list they have for people with "chronic melanoma."

I chose to drive more than an hour, and still I've had to wait another five weeks for the appointment. This is just one of many examples of Kaiser's actual dealings with patients, which I've written about before. 

The contrast with the advertisements is astounding.

The person on the phone was nice. She explained as well as she could, but it wasn't enough, because the system is not really there to take care of people's medical needs. And there's no way she could explain that---but that was okay, because I already knew it.

Medical Advice

I just read an online article, "Here's What Experts Say about the Advice on Dr. Oz and The Doctors," which states what should be obvious to all of us:

A lot of this advice is pure garbage.

From the article:

"Reporting in the BMJ, Canadian researchers analyzed two medical TV talk shows—The Dr. Oz Show and The Doctors—and found that only 46% of the recommendations on The Dr. Oz Show and 63% on The Doctors were supported by evidence. 15% of advice given on Oz and 14% of advice on The Doctors contradicted the available published evidence in journals."

Dr. Oz's excuse, given to a Senate subcommittee hearing in June 2014 was, according to the article:

“I do personally believe in the items that I talk about on the show. We have to simplify complicated information. We have to make the material seem interesting and focus on the ‘wow’ factor.”

And that probably sums it up really well. "...the 'wow' factor." Because it's TV, it's entertainment, it's not real medicine.

But I think another problem here, the reason people are watching these shows, is that people are reluctant to talk to their own real-life doctors about problems that are embarrassing.

Another problem might be that they don't trust their own doctors to take the time to really listen and understand their concerns. I mean, we've all been to a doctor who barely listened to what we said, haven't we? Who grabbed our chart from the plastic chart-holder outside the room and walked in reading it for the first time, glanced at us, and started probing us without even washing his hands first? Who made us wait more than half an hour and then could hardly wait to get to his next patient?

(I'm using male pronouns here because most of the doctors I've encountered who acted this way were males, not because female doctors don't do it!)

But here's another thing: Is the advice we might receive from our own doctors any better than the tidbits from the TV shows?

Haven't you been seen by a doctor who gave recommendations that were not supported by evidence? I have. (And, yes, it was a male doctor.)

What's a person to do? I'm still thinking about this. Any suggestions?

Madame L and the Third Person Pompous

Dear Readers,

Madame L is as of now swearing off her use of the persona who writes pompously in the third person (as she is doing now).

So, okay, here goes. I'm still the same person; I'm still calling myself, while writing this blog, Madame L; but I'm going to write just plain old English from now, instead of what I have decided to call the "third person pompous."

I'm going to be writing about news in science and medicine, arts and culture, environmental issues, and whatever else comes to mind; and I think these issues deserve better than the semi-humorous way I was writing before.

The first thing I want to mention is that after not writing on this blog for a few months, coming back to it today was an eye-opening experience as I had pages and pages and PAGES of "Anonymous" comments to scroll through. And I mean, really, I just scrolled through them, after quickly dividing them into a few types:

---Scams hoping to get me to click on some link that would crash my computer;

---Scams hoping to get me to click on some link that would bring me to a site with images I would never want to see and then crash my computer; and

---Scams hoping to get me to click on some link that would bring me to a site where I might think I was purchasing some drug, for instance a virility-enhancing drug, which I could not obtain legally, and then crash my computer.

But, wow, was I ever flattered by the scammers who wanted me to believe they had never seen a blog as amazingly intelligent and insightful and well designed as mine, and to believe that all they needed and desired most in life was for me to offer to help them with their site, which would ... then crash my computer.

Sarcasm? Oh you bet! And the old Madame L would surely approve!

Thanks for reading (and commenting, not anonymously),

Madame L

The Sunday Book Review: August 3, 2014: The Psychopath Whisperer

Madame L found this book in her local library---after being put on a "Hold" waiting list for several weeks---and highly recommends it to any of her Dear Readers who are interested, as Madame L is, in these people who lie, steal, assault, and kill, all without conscience or remorse.

In fact, the subtitle of the book is "The Science of Those Without Conscience," which describes those people we call psychopaths as well as those we call sociopaths very well.

Madame L has been reading up on the subject in an attempt to understand these people, but what she has found is that, as Walter Kirn wrote in "Blood Will Out," it's impossible to know what goes on in their minds. In fact, Kirn said in a post-publication interview:

As a writer it was my good fortune [to know Christian Gerhartsreiter]. As a person it was my bad fortune. As a writer, it gave me insight. But no one would voluntarily spend this time with a psychopath. No one would voluntarily let their life get enmeshed with a murderer or someone capable of chopping up a body and burying it. It was truly traumatic to realize I was somebody whose weakness for a good story and whose ability to tell a story to himself, really put himself in danger.

The author of "The Psychopath Whisperer," Kent A. Kiehl, PhD, is the first author on this subject that Madame L has read who is really qualified to write on the topic, as he has spent his entire career, beginning as a graduate student, trying to figure out why these people do what they do.

And, guess what: For those who can really be called psychopaths, it does come down to a difference in the brain structure. Psychopaths have reduction of grey matter in the paralimbic system, which leaves them with no empathy. 

Here's a YouTube video featuring Dr. Kiehl, who is now at the University of New Mexico.

But what makes this book worth reading is not only the information on the human brain and how it affects our emotions and behavior, but all the incidental facts and stories from Dr. Kiehl's career. And this works because Dr. Kiehl is a good writer. He knows how to tell a story, for sure---beginning with his first day at a maximum-security prison where he began his studies---and on through even details about brain-imagining machinery which most other authors would make boring beyond belief.

(The grammarian in Madame L hastens to add that Dr. Kiehl knows how to write a complete sentence with good grammar and correct spelling. Amazing! This is the first book Madame L has read in a very long time which did not tempt her constantly to be making editing notes in the margins.)

And here's a YouTube video with more information about differences in the brains of psychopaths: