Monday, May 21, 2018

Academia is failing and everyone is responsible

I chose to retire early because the academic environment I was in had become toxic. And not just for me.

In addition to working 9-10 hours, sometimes more, and having a four-hour daily commute, the academic environment had become dysfunctional. In addition to experiencing discrimination, increasing (often unreasonable) demands, incompetence at all levels of administration, support and guidance was not only lacking, but often there was no accountability. Many PIs lacked people and group management skills, department heads often overlooked bad behavior and management, and too many times the university Human Resources either overlooked or refused to intervene when valid complaints were reported. This lack of accountability only enabled poor lab environments at the expense of productivity, quality research, and satisfaction by all lab members. Education also suffered collateral damage.

In the capacity of most of the strata of that hierarchy (except as department head and institutional office) over several decades, I have seen many bright and capable students, staff, and even PIs, leave academia. I (and a colleague) left one university because of discrimination, harassment and a very dysfunctional department. I finally retired from another university after ten years with similar experiences. During that time I worked with a few colleagues that had exceptional people and management skills, and who also left for other positions and institutions. With sadness, and some anger, I have also seen productive graduate students with excellent potential also leave. Most eventually found a favorable position and institution, but a few left science completely because of their bad experiences.

The culture and system is deteriorating at all nodes and needs attention. I am encouraged to see some attention to these matters in the last several months in a few reputable journals and on social media, especially blogs. However, the focus has been on graduate students, especially post-docs. But that attention and concern needs to broaden out to include PIs, department heads, and institutional management.

Yes, the fault is spread everywhere in the system. So let’s include every participant.

The group at the journal Nature recently posted a poll on their FaceBook group page, Nature News and Comment.

The following was my comment to this poll about people management training in academia:

“I chose “Additional training for PIs” because:

1. I could choose only one.

2. The established hierarchy of the academic unit is PIs at the top. A PI with good skills with people and work management, especially communication, will potentially already establish and maintain a healthy and productive lab environment. That includes training of lab assistants and students.

Additionally, students (and other lab staff) often feel powerless when department heads and even Human Resources do not provide guidance or intervention when complaints are reported. In those cases, the PIs weld complete authority.

3. After perusing the articles in Nature and other journals on this topic, most of the attention is on graduate students. Lacking is focus on improving skills for PIs and the overall members of the culture (including department heads and administration). Glaringly absent is recognition of lab assistants, especially lab managers, who often are the surrogate lab nanny and educator.

Being retired has allowed me to reflect on the past 28 years serving in the capacity of all points in that hierarchy (except department head). At each node is the ability to contribute to a healthy, productive, and satisfying academic experience and culture for all.

However, it seems that the appropriate skills have deteriorated, and awareness of that has fared even worse over the last two decades. Academia and the culture, including the institutional, have generally but not universally deteriorated, with both education and research suffering. I have seen many bright graduate students and PhDs leave (myself included). And it needs “fixing” at every node in the system.

Why place the burden solely on the students?”

Sunday, May 20, 2018

As you think we know........

Thetis: “Why then, child, do you lament? What sorrow has come to your heart now? Tell me, do not hide it in your mind, and we shall both know.”
Achilleus: “You know; since you know why must I tell you all this?”
The Iliad, Book I

As a writer I really have few ‘pet peeves’. If you place a comma in the wrong place, if you use quotation marks instead of apostrophes, or other slights and ambiguities of punctuation, we still get your meaning. If you weren’t raised on the Strunk and White bible, “Elements of Style”, don’t stress it. Strunk be damned and White was a hypocrite (he himself advocated ignoring his manual). As long as you use appropriate periods and spaces, you can get your message across. We really don’t have to be style Nazis.

However, a pet peeve that I do have, or it has me, is overuse of “As you know.....” or “As you already know.....”. YES WE ALREADY KNOW! Or NO, STUPID; HOW DO YOU EXPECT US TO KNOW?!

It’s a tropism used in writing fiction; a literary tool to give information or explain something to the reader that they don’t know otherwise, or have forgotten. But it has to be used carefully and not assuming that the reader (or audience) doesn’t know or does know where the lead in is going. But if the writer, or speaker, assumes that the reader or audience knows, and when that assumption has a high probability of being wrong, THEN DON’T USE IT! Recall that commonly used cliche! “‘Ass-ume’ makes an ass out of you and me.”? Well, it makes more of an ass out of the person that assumes, and it irritates the hell out of the ‘me’.

I see the use of this misplaced trope much too often on blogs and other social media, especially posts on FaceBook. “As you know, I moved across the country to this location.” I think to myself, ‘If you know we know, then why tell us that we already know?!’ It makes me want to shake the writer, or pull a Gibbs and smack the writer on the back of the head (TV series NCIS reference). Don’t use this trope unless you are writing a novel!

I have heard this trope used in some presentations, but it is placed well as a segue or to invite a question from the audience. Example: “As some of may know, not all grasses use the same photosynthetic pathway. Some species use the C3 pathway, others may use the C3 and C4 pathways.” Assumptions that all those in the audience know this is not implied, and the speaker explains a setting for the rest of his talk.

If you are writing a novel or short story, and a character needs to fill in a gap, this trope can be handy in dialogue, such as the example above of the speaker’s use, or to refresh the reader’s memory of an immediate and pertinent point. It can also be used to imply character personality, especially arrogance, such as with the famous character of Sherlock Holmes.

But if you don’t want to appear arrogant or pretentious, then DON’T USE IT!!

Wednesday, May 16, 2018

Judges Playing Scientists

Superior Court Judge Elihu Berle, argued that roasters and manufacturers failed to prove that that there is no substantial risk to drinking coffee, or that the benefits of drinking the beverage outweigh the risks posed by acrylamide, a substance created naturally during the brewing process. By the standards of California’s decades-old Proposition 65 law, Berle affirmed in his final ruling last week, all coffee sold in California must come with a warning label stating: WARNING: This product contains chemicals known to the State of California to cause cancer and birth defects or other reproductive harm. *

An example of scientific ignorance and misguided judgement.

If coffee should be labeled as carcinogenic, then so should toast, grilled meat, pizza crust, and a plethora of other foods that contain a lot of carbohydrates and proteins.

BUT it is ‘okay’ to ingest foods that have been exposed to pesticides demonstrated to be neurotoxins and carcinogens, and drink water tainted with the same, without the same warnings!

The Maillard reaction that occurs during heating or breakdown of certain substrates does produce acrylamide (and free radicals). It is basic organic chemistry. Is it carcinogenic? It can be, depending on dose and the animal. This is based on experiments with mice, but not with humans. Although mice are not men (murine models have limitations for extrapolation to humans), using mice can lead to suggestive conclusions that then must be tested in humans. Pharmacology history is fraught with failures in extrapolation from mice to humans.

Should we be concerned? Possibly, if you are drinking a gallon or more of coffee every day. The greatest threat from anything involving the Maillard reaction products, including acrylamide, is smoking! And uncontrolled blood glucose levels.

The Maillard reaction that occurs from smoke inhalation and rampant metabolism of glucose and proteins in tissues causes exceedingly high free radical production and Amadori products which accelerate breakdown of connective tissue in the body (elastin and collagen in skin, tendons, ligaments, vascular tissue, eyes, etc.). That’s why smokers have accelerated aging of their skin, and it is a contribution to diabetic pathophysiology.

We shouldn’t expect judges to be scientists, but we should expect them to consult with experts in the field in which rulings are concerned.

Interesting that they don’t exert the same concern and rulings with documented toxins in our environment, other than those spurious claims.

* In Labeling Coffee a Carcinogen, California Leaps Ahead of the Science

Monday, April 09, 2018

Is life is like Play-Doh?

On the tail of the silver fox.......

Despite that the field of epigenetics is often dismissed as a fad topic, that may come back to surprise us, just as the derision of ‘junk DNA’ did several decades ago. 

Similar to the silver fox domestication project, scientists in Sweden replicated domestication of red jungle fowl (ancestors of modern chickens) and selected for fear of humans tameness. After five generations, they examined changes in the genetic structure associated with certain phenotypic traits, especially behavior.

Behavioral traits are associated with many physiological and neural mechanisms. Signaling compounds in the body involved with these processes are dopamine, glucocorticoids, epinephrine, and many others. All of these signaling molecules are synthesized in tissues and organs, such as they hypothalamus. Based on prior studies, the research team examined changes in the hypothalamus of  their test subjects. They discovered that not only were DNA methylation patterns associated with cellular metabolism and neural signaling, but there were sex-specific changes.

In agreement with other similar studies of selection pressure during domestication, this study adds further evidence that changes in genetic structure are related to the driver(s) of selection for specific traits, such as egg size in a breed of domesticated chickens.
“This suggests that different selection pressures generate distinctive sets of epigenetic changes, which in turn are related to specific phenotypic traits.”
Epigenetics may have increasing importance now because of its suggestive role in phenotypic plasticity, which often precedes adaptation to environmental change. Understanding how organisms respond to selection pressure can help us better model and predict the fates of many species of concern in this age of rapid climate and anthropogenic changes. Including our own.
“Our results suggest that bidirectional selection for tameness involves epigenetic factors that can even differ in a sex-specific manner. Observation of divergent DNA methylation patterns in the hypothalamus after only five generations of artificial selection highlights the importance of epigenetic mechanisms, in addition to genetic composition, in evolutionary phenotypic variation that emerges in response to selection pressures.”

A researcher in Europe has been studying these association based on changes in gene expression in melanin, phenotype, and behavior adaptation in owls. Ironically, humans have unknowingly been experimenting in this for thousands of years by our own selection for domestication of many plant and animal species.

Friday, March 30, 2018


Long quote for the.......... (choose arbitrary time line).
This one is a keeper.

“2. I mostly don't often admit this, even to myself, but at times I can't ignore it. Movies really suck. Most books. Most music; art, architecture, civil planning, project management, military strategies and politics are awful. They are ill conceived and poorly implemented. We've gone to the trouble to document the hard earned learnings of our lengthy civilization only to set them aside, all over again, every generation. 

It can be awful to sit in a restaurant alone and overhear random people chatting. Many are self-centered and infantile, focused on all the wrong things, misunderstanding what matters and how things work. They scar their own children unaware and make choices that can only harm themselves in the future. Meanwhile, outside the window, the cumulative cost of a huge and powerful society of mental middle-schoolers is baring down on us. Our society not only denies truth, it acts to suppress it; to rewrite it, but that only insures we will lose eventually.

We require money to feed ourselves, so off to work we go. You do not pick your co-workers or bosses. Diversity is important and powerful, but nature loves a bell curve, so you know some of the people you interact with will be the sports and celebrity chat show set. You soon discover that people do not pick leaders for intelligence or maturity or wisdom. You know you will be tasked with inefficient, unhelpful work. You know that when you see change coming, you cannot say so, because they hate you more for being right than for being wrong. Sometimes, you know more about a person than they know about themselves. They don't realize that the messages their subconscious sends out are perfectly clear.

So, the second point is, yes it can be seriously depressing to be ruled by corrupt children, fed on junk, surrounded by monuments to poor decisions and weak literature.”

(Really excellent post and very long but enlightening, somewhat entertaining, thread of comments.)

Friday, March 16, 2018

No Single Diet for a Big Planet

The increasing pressure for everyone to convert to a vegan diet smacks of ignorance and righteousness. Yes, that includes scientists, and shame on them.

This stated universal solution for the health of everyone on this planet and all the ills of climate change is fraught with negligence to the fact that not every person can subsist in good health on a vegan diet. Nor is it necessary (some bold scientists have published data on why).

While the public, and many scientists, claim that adopting a vegan diet is the most important way to lose weight, be healthy, reverse climate change, and treat the planet better, there are reasons to believe this isn’t always the case. Despite the prevalent binary thinking and judgement of our Western society, fad science, and culture, there is no one, universal, de facto “right” diet for everyone. Our genetics, physiology, medical history, economic status, food accessibility, and aesthetic tastes are vastly varied. Absolutisms are rarely absolute.

Many people have food sensitivities and/or allergies: allergies to peanuts, gluten-related disorders (including wheat allergy and insensitivity to fructans), intolerance to yeast and/molds (such as in leavened breads, beer and several cheeses), phytates in many legumes and vegetable (taboo for people prone to kidney stones), “onion intolerance” (sensitivity to ingestion, even dermal exposure, to one or more plants in the Allium family), fructose malabsorption (bad things happen when eating even a small amount of most fruits), legume (including soybeans) intolerance/allergies, and the list goes on. People with these sensitivities and allergies may be unable to commit to a vegan diet without jeopardizing their overall health.

Another topic rarely seen in the lay media, and uncommon in the scientific literature, is the nutrient efficiency of a diet containing even a small amount of animal products - meat, milk, yogurt, cheese, eggs. By comparable weight, animal food products contain more protein (especially in the context of complementary amino acid profile), bioavailable minerals, and energy than any non-animal product. 

The cautionary point here is that most of the consumed energy is in the form of lipids, aka ‘fats,’ especially cholesterol. Primates -yes, us, too- evolved to store dietary fat for emergency energy in cyclic periods of famine. However, in our modern world of convenience and accessible plenty, we no longer need as much, and eat too much of it. Also, removing excess fat and eating naturally lean meat is an alternative.

The loud proclamation that everyone should embrace a vegan diet is unwarranted and impossible for many people. Nor should the reason of significantly reducing our carbon footprint be justification for imposing guilty consciousness. Some people just can't adopt a vegan diet. Moreover, a universally adopted vegan diet will not solve the demand for food and reverse climate change. 

Research at the USDA-Agricultural Research Service found that removing animal protein from the diets of many people would increase nutrient deficiencies that have been associated with certain health risks, like cardiovascular disease. Mary Beth Hall, animal scientist and one of the study researchers  at the U.S. Dairy Forage Research Center, comments in a press release,
“Different types of carefully balanced diets — vegan, vegetarian, omnivore — can meet a person’s needs and keep them healthy, but this study examined balancing the needs of the entire nation with the foods we could produce from plants alone. There’s a difference between what’s possible when feeding one person versus feeding everyone in the U.S.”

More importantly we should put more emphasis on growing some of our own or buying locally produced food, learn to make better food choices, eat balanced meals of both vegetables and animal products, plan meals centered around seasonally available foods, and stop piling so much food on our plates. 

Oh, and spending less time on our devices, in our vehicles, and getting off our butts and moving around around would not only reduce our appetite, improve our health, and possibly shrink that carbon footprint. Add supporting informed policy change at the local, state and national levels, too.

Sunday, March 05, 2017

Sobering thoughts for a Sunday morning

"We have become the United States of Spite, and we are in this condition because it serves the interests of the plutocrats to have us at each others throats as our quality of life disappears upstream.

This new administration has set about undoing every good thing government has done for us, one vile rescission after another. And they do it with a righteous glee that sickens me. They do it with a logic that is not logic, using facts that are not facts. And they're cheered on by people who are likely to be among their worst victims.
It's hellish."