Stan Fields – Genes to Genomes https://genestogenomes.org A blog from the Genetics Society of America Mon, 03 Apr 2017 18:55:46 +0000 en-US hourly 1 https://wordpress.org/?v=6.6.2 https://genestogenomes.org/wp-content/uploads/2023/06/cropped-G2G_favicon-32x32.png Stan Fields – Genes to Genomes https://genestogenomes.org 32 32 Is science of value? https://genestogenomes.org/is-science-of-value/ Mon, 03 Apr 2017 17:14:43 +0000 https://genestogenomes.org/?p=8698 I had hoped that it would be a bit of cheery news that dragged me out of retirement from this blog to subject you to another edition of frameshifts. Alas, no. Instead it is the war on science that compels me again to set electrons to screen. The narrative that has become popular in some…]]>

Frameshifts LogoI had hoped that it would be a bit of cheery news that dragged me out of retirement from this blog to subject you to another edition of frameshifts. Alas, no. Instead it is the war on science that compels me again to set electrons to screen. The narrative that has become popular in some circles is that research is the province of pointy-headed intellectuals in a few left-wing college towns. And, continuing this logic, if these elite eggheads get a few less tax dollars with which to putter and pontificate, nobody will be any poorer. Furthermore, if the findings and advice of scientists are ignored, well—why should a scientist’s version of facts be accepted any more than anybody else’s? We, as practitioners of the scientific profession, need to combat this narrative.

Let’s take these points in turn. Where is science carried out in this country, and who does it? Americans are hardly aware of the impact or import of scientific research, even when it’s going on right next door. When Research!America asked if “medical research in the U.S. is conducted in all 50 states,” a mere 21% of American adults said “Yes” (the most frequent response, from half of those polled: “Not sure”).1

Research goes on throughout the country. Consider a state—any state; let’s say Georgia. In 2015, it received more than $500 million in NIH funding, more than $150 million from the NSF, more than $40 million from Department of Agriculture research funding, and nearly $10 million from the Office of Science at the Department of Energy.2 From the NIH alone, Emory, Georgia Tech, Georgia State, Georgia Regents (now Augusta), Morehouse and the University of Georgia each brought in more than $20 million—some of these way more. 3

Who benefits from this scientific activity in Georgia? It’s estimated that NIH funds directly support more than 10,000 jobs and $1.5 billion in economic activity in Georgia 4. Add to that number more than 25,000 people in Georgia who work in the biopharmaceutical industry (many of these folks likely trained in nearby research universities). And I’d venture to guess that all this economic activity doesn’t account for the coffee shops, daycare centers, gyms, take-out restaurants and other businesses that sprout up next to major medical centers and biotech companies.

Will it matter much if support for research is cut—to the tune of about 20% (or even more) at NIH, DOE, EPA and other agencies that fund science? Let’s play out the President’s plan that would enact this level of budget cuts. Many labs will close down, in Georgia—in cities like Atlanta, Athens and Augusta—and in other states, in cities like Indianapolis IN ($133 million from the NIH), Lexington KY ($102 million), and Columbia MO ($42 million). It seems certain that scientists in all 50 states will lose jobs.

But beyond the effect on employment, many of the sensational research findings routinely discovered in American labs, and that all Americans—whose tax dollars support these labs—are rightly proud of, will instead occur in Europe, China, Japan and elsewhere. Those findings in labs far from our shores will spawn the patents and intellectual know-how that lead to new industries with their well-paying jobs, jobs created in perhaps Saskatoon, or in Seoul, or in Sydney, rather than in any American city. Perhaps the hub of some future industry built on the results from basic research ends up in Stockholm or Amsterdam, instead of in our next Silicon Valley.

How will the young, smart, creative Americans who populate our graduate and postdoc programs, and the many bright international scholars who contribute to our research teams, respond to these Federal cuts? Seeing the low priority that this country places on science, talented Americans will seek alternative careers with better long-term prospects; scientists in other countries will choose to train elsewhere rather than the United States.

Will there be ramifications if scientific views are ignored? The ease by which research funding provides such a convenient target for reducing Federal spending may be a result of our country’s diminished scientific literacy and loss of respect for expertise. Ultimately, the consequence of the notion that all viewpoints are equally valid is decision-making that defies the overwhelming consensus of scientific data. Recent actions of the President to weaken fuel efficiency standards for cars and trucks and to eliminate plans to cut emissions from coal-fired power plants fit neatly into the myth that there is no scientific consensus about human-caused climate change. The result will be water that is dirtier, air that is smoggier, a planet that warms ever faster. Choosing an EPA head who thinks that carbon dioxide does not contribute to global warming will not convince Mother Nature to change her laws.

All of us need to stand together for science and make our voices heard. We need to contact our local members of Congress, write op-ed pieces and letters to the editor, talk to our friends and neighbors. And join with me and scientists around the country in the March for Science on April 22nd, for which the GSA is a sponsor. The future of our profession, the prosperity of our nation, and the health of our planet depend on our actions.

 

1https://www.researchamerica.org/sites/default/files/RA-PDS_Vol17_FINAL.pdf
2 http://www.faseb.org/viewer.aspx?id=122&Name=Federal-Research-Funding-in-Georgia.pdf
3 https://report.nih.gov/award/index.cfm
4 http://www.unitedformedicalresearch.com/state-by-state/#state/georgia

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Even though Gregor Mendel asks not to be rediscovered when he hears us… https://genestogenomes.org/even-though-gregor-mendel-asks-not-to-be-rediscovered-when-he-hears-us/ Thu, 15 Dec 2016 17:00:09 +0000 https://genestogenomes.org/?p=7929 To paraphrase the Car Talk guys, “Well, it’s happened again—you’ve wasted another perfectly good year reading frameshifts.” Although not as much as I have in writing it. And perhaps this hasn’t been “perfectly good” as years go. But as far as the GSA goes, we’ve dealt with some major events this year.     First,…]]>

Frameshifts LogoTo paraphrase the Car Talk guys, “Well, it’s happened again—you’ve wasted another perfectly good year reading frameshifts.” Although not as much as I have in writing it. And perhaps this hasn’t been “perfectly good” as years go. But as far as the GSA goes, we’ve dealt with some major events this year.

 

final timepoint

 

First, we organized a successful TAGC meeting in July of more than 3000 participants, bringing together seven of our core constituencies. TAGC has caused us to think more about what type of conference best serves our interests as geneticists. If we held another TAGC, would we do better with most of the sessions organized around biological themes rather than have them centered on the experimental organisms? Or would this framework lose too much of the organism-specific focus that has been a popular feature of our traditional meetings?

Second, we celebrated the 100th anniversary of GENETICS with a host of special articles and commentaries, all on a revamped website with a new look of the journal. And G3 continues to gain in reputation and submissions.

Third, we hired a new executive director—Tracey DePellegrin—who is reshaping the staff and procedures for GSA in Bethesda and Pittsburgh. Tracey brings an energy and intensity to our activities that have me excited about what our society can accomplish in the future. Look for upcoming changes to the GSA website, expanding topics on our communications platforms, and a new look for G3. And while largely invisible to members, our infrastructure—including finance, IT and space—is undergoing numerous improvements that will allow us to better work for you.

Fourth, our board of directors and staff have engaged in discussions throughout the year about what should be our essential mission as a society, especially in this time when the usual reasons for joining a scientific society carry less weight, and with our journals, communications, conferences, web content and the like widely available whether or not you’re a member. As a result of these discussions, we came to appreciate that we need to address better what we do for our graduate student and postdoc members. We hired Sonia Hall to head up this effort, and we need to hear from you about what you’d like the society to take on in this area.

The GSA, however, does not exist in a vacuum, and of course we look with concern to the role of science in the future of the US and the rest of the world. Are we in for an extended period of time when scientific expertise is ignored—or worse—disbelieved? Is each person entitled to a unique version of the basic facts about nature? Does a concern, maybe a misguided one, for jobs and corporate profits mean that we turn a blind eye to planetary disaster under the disingenuous guise that “the science is still unsettled”?

It was dispiriting to see the fragmentation of America exposed by the recent vote, the uneven patchwork of red and blue districts. What can we do as geneticists and scientists to heal the rifts between us? What can we do to prevent each of us from adopting a worldview colored almost exclusively through the messaging that comes to us from like-minded individuals? How do we get the idea across that—genetically speaking—human beings are more alike than different, and that the great bulk of the genetic variation in us is found in all population groups? Tough questions, with no easy answers.

It seems to me it is especially important right now that scientific societies like the GSA are supported, so that we can act as united communities. For this reason, I urge you to renew your GSA membership for 2017, or to join us for the first time. We need geneticists to have a strong voice communicating with the world outside our labs. Even more, we need your involvement and your passion, because we have only a small staff and the limited time of our volunteer leadership. But our challenges—in enlisting support for basic research, in providing authoritative information on genetic subjects, in boosting our trainee activities—while continuing to publish two well-respected journals and to organize conferences at which many young scientists make their first presentations, are enormous.

Finally, on a personal note, with this last post I need to point out that frameshifts could not have happened without a lot of help. I am particularly appreciative of Retrosleep, my cartoonist, who turned vague images and scrawls into drawings, and Mark, my chief editor, who smoothed out a lot of prose. On many posts, I benefitted from comments or edits from Tracey, Cristy, Lynn, Jasper, Doug, Christine, and Eric, and cartoon ideas from my lab (especially Matt, Stephanie and Ben) and from my son Paul. Thanks to Vijay, Ian, and the two Janes for their work on the G&S spoof. Please keep GSA-art coming—we’d love to see examples of writing and crafts along with artwork. Like any author, I was delighted when a post elicited comments from you, my readers.

Though my term as president soon comes to an end, and Lynn Cooley—who has been a wholehearted partner with me on all of this year’s GSA initiatives—takes over the society and frameshifts, I reserve the right to write new posts from time to time, if the muse strikes. To reprise the theme of my first post from January 1, it’s a wonderful time to be a geneticist, and I thank you for allowing me to serve as head of this remarkable and venerable society. And don’t drive like my brother.

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Did you know they rewrote the game? https://genestogenomes.org/did-you-know-they-rewrote-the-game/ Thu, 01 Dec 2016 13:00:40 +0000 https://genestogenomes.org/?p=7848 If you’re a young geneticist who spends most of your life hanging around universities—as I still do—you’ll likely notice in your department the presence of some old people. People in their 80’s and 90’s. Often, these are scientists who made incredible discoveries decades before you were born, but you may not know a thing about…]]>

Frameshifts LogoIf you’re a young geneticist who spends most of your life hanging around universities—as I still do—you’ll likely notice in your department the presence of some old people. People in their 80’s and 90’s. Often, these are scientists who made incredible discoveries decades before you were born, but you may not know a thing about their accomplishments. My advice to you before you find you’re moving on to another locale: invite one of these folks for a cup of coffee and treat yourself to a wonderful conversation. You may even find yourself relaxing a bit as you learn that science—as well as the larger world in which it exists—has always gone through periods of uncertainty and upheaval.

That those new to a field don’t know the history of their field is unsurprising and not necessarily a bad thing. It’s far more interesting to push the scientific frontiers of today than to spend time learning how challenges of long ago were overcome. But there is a lot of value in taking a few minutes to meet some of the codgers who confronted those challenges in their youth.

 

older-scientist-560

 

 

I first noticed old scientists when I was a graduate student in Cambridge, England in the 1970s. At that time, Lord Adrian (then 87), an electrophysiologist who won a Nobel Prize in 1932, could be seen walking across the lawns at Trinity College. At seminars in the Cambridge University Department of Biochemistry, where I did a course for the final undergraduate year called Part II, several old men with thick glasses sat in the front row; although it had been a long time since they were active experimenters, these men had discovered some of the fundamental reactions of biochemistry. But I never talked to Lord Adrian or any of the other senior biochemists.

As a young faculty member at Stony Brook in the late 1980s, I occasionally would see 1983 Nobel Prizewinner Barbara McClintock (then in her mid-80s) at Cold Spring Harbor Laboratory. Given the scarcity of women leading laboratories in the 1930s and 1940s, McClintock was a rare example of an old scientist who was a woman. But I never got to know Barbara McClintock.

Now that I’m starting to get up there in years myself, I’m in an enviable position. I have no inhibition about talking to our most senior faculty at the University of Washington, because these are people with whom I’ve been colleagues for a couple decades plus. Let me introduce you to a few.

Stan Gartler, 93, in Medical Genetics and Genome Sciences, used the phenomenon of X chromosome inactivation to show, in the mid 1960s, that tumor cells are clonal, arising from a single cell; Stan won the McKusick Award this year from the American Society of Human Genetics. George Martin, 89, in Pathology, looks a whole lot younger, maybe not unusual for someone who undertook some of the first genetic approaches to the study of aging. George just received a 5-year grant from the NIH and hopes to be still funded at 100. And Eddy Fischer, 96, in Biochemistry, with his colleague and co-winner of a 1992 Nobel Prize, Ed Krebs, discovered reversible protein phosphorylation in studies begun in the mid 1950s. I’m delighted to say that I’ve recently had enjoyable conversations with each of them.

If you’re hoping to find out the latest methodological wrinkle in Somekinda-seq, don’t start out with your local octogenarians and nonagenarians. But if you want to learn a little about how to find a tough problem to solve, or how to work with collaborators who push you in different directions, or how to combine methods from diverse fields, or how to persevere through difficult failures—these senior scientists are priceless sources of information. Some of them can tell you the history of scientific events that changed the way biological research is done. Others can describe the early stages of a method or apparatus or concept that will give you hope when you tackle the odds in coming up with one of these today.

Old members of our community have also seen the country and the world go through smooth times and rocky times, only to emerge again united in purpose; take advantage of their wisdom. And don’t underestimate the ability of older generations to learn new science. They will appreciate hearing from you what has come of the fields they set in motion long ago.

So get over your trepidation of approaching someone whose birthday cake might illuminate a stadium for Monday night football. Engage them in a conversation. Please let me know if you’re happy with the outcome.

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Another letter to Mr. Trump https://genestogenomes.org/another-letter-to-mr-trump/ https://genestogenomes.org/another-letter-to-mr-trump/#comments Fri, 18 Nov 2016 13:00:16 +0000 https://genestogenomes.org/?p=7761 Dear President-elect Trump, It’s me again. I wrote you last week to say why you should make science a cornerstone of your administration. Don’t feel bad that with all the hubbub of starting up your new job, you haven’t had a chance to get back to me yet. But as I’ve read about some of…]]>

Frameshifts LogoDear President-elect Trump,

It’s me again. I wrote you last week to say why you should make science a cornerstone of your administration. Don’t feel bad that with all the hubbub of starting up your new job, you haven’t had a chance to get back to me yet. But as I’ve read about some of your likely choices for cabinet posts and advisers, I want to write to you again before it’s too late.

The American people will soon rely on you to sustain our natural ecosystems—clean water, breathable air, unspoiled public lands and all the species, including us, that depend on these resources. I urge you to appoint people with substantial expertise to your cabinet, regardless of their political philosophy. Experienced administrators with the long-term interests of the entire nation at heart are likely to make decisions that both you and I—and more importantly, our children and grandchildren—can live with. For example, William Ruckelshaus was appointed as administrator of the Environmental Protection Agency by Richard Nixon, and then a second time 10 years later by Ronald Reagan; in 2015 he received the Presidential Medal of Freedom from Barack Obama.

But when I see that contenders for your key environmental positions include those who have served as lobbyists or executives for industries—like oil and gas—that they will regulate, I struggle to find the correct term for this phenomenon. Recalling your campaign promises, I am sure you have no desire to inspire the new slogan: refilling the swamp. It will be near impossible for individuals whose loyalties are one-sided to be effective stewards of the environment.

By contrast, fair-minded environmentally-aware appointments seem far more likely to promote the sorts of policies that will stimulate new industries and generate new jobs. Renewable energy can provide long-term jobs, whereas the future of coal is limited. You need only look at the air right now in India to see what awaits those who fail to pursue clean energy.

It is particularly disconcerting to us scientists that you are considering as EPA administrator someone who leads a group that is “focused on dispelling the myths of global warming.” In the focused intensity needed right now to put together an administration, perhaps you have not had sufficient time to review the scientific evidence for climate change. If you can find a few minutes for this, my fellow scientists will provide you with digestible data to examine; a large fraction of the more than 300 million residents of the US and 7 billion on the planet will think your time considering findings and recommendations from climatologists well spent.

It’s worth remembering that ignoring scientific evidence and professional competence by appealing only to your most science-skeptical and regulation-averse supporters can exact a steep price.

James Watt, a Secretary of the Interior in the 1980s, said back then that, “We will mine more, drill more, cut more timber”*, as he advocated reduced regulations on oil and mining and sought to open up wilderness areas to oil and gas exploration. Watt resigned fewer than three years into the job after a highly controversial tenure. He did, however, make Time magazine’s list of modern history’s top 10 worst cabinet members.

Anne Gorsuch, an EPA administrator also in the 1980s, cut the EPA budget and personnel, relaxed air quality standards, and encouraged the use of pesticides. It may be relevant to today’s politics that she, too, hired staff who came from the very industries that they were being hired to regulate. But Gorsuch refused to provide Congress with documents related to charges of mishandling funds for toxic waste clean-up and was cited for contempt of Congress. She resigned after less than two years on the job.

And perhaps you recall Michael Brown, director of the Federal Emergency Management Agency, who presided over the 2005 response to Hurricane Katrina as it devastated Louisiana. That presidential administration took a severe hit to its stature from Brown’s actions.

During the recent campaign, there was hardly any discussion of the environment. Thus, while those who voted for you may be persuaded of your vision to bring back jobs and eliminate trade agreements, they cannot be said to have endorsed the view that climate change is a hoax. Many of them understand that it is real and that it is a danger. A Pew survey found that, “More than three-quarters of Democrats and most Republicans…say climate scientists should have a major role in policy decisions related to the climate.”

Nothing from the recent election suggests that the majority of the American people support a desire to pollute the planet more drastically or to promote an increased use of fossil fuels that will lead to devastating droughts and floods.

Mr. Trump, you have the rare chance to be acclaimed by the world’s citizenry as the man who saved the planet when many expected that you might destroy it. Seize the opportunity.

Respectfully,

Stan Fields

 

Those of you who have similar concerns should write your own letters to the new administration, and encourage your colleagues to do so as well.

 

*widely quoted in mediatransparency.org but site no longer exists

 

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Dear Mr. Trump https://genestogenomes.org/dear-mr-trump/ https://genestogenomes.org/dear-mr-trump/#comments Fri, 11 Nov 2016 16:30:19 +0000 https://genestogenomes.org/?p=7669 Dear President-elect Trump, Congratulations on your victory. As a fellow president myself (albeit with a much smaller constituency), I can remember well those early post-election days, when the surge of heady enthusiasm for all those things I hoped to accomplish had not yet been eroded by the practicalities of actually governing. But as a geneticist…]]>

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Dear President-elect Trump,

Congratulations on your victory. As a fellow president myself (albeit with a much smaller constituency), I can remember well those early post-election days, when the surge of heady enthusiasm for all those things I hoped to accomplish had not yet been eroded by the practicalities of actually governing. But as a geneticist writing to a man of business, I’d like to tell you why you should surprise the world and make science the cornerstone of your administration.
whitehouse-550

 

First, science and engineering create jobs—good jobs. In my world, it’s pharmaceutical companies making antibodies to treat cancer, or biotech companies using stem cells to regenerate tissues. In other fields, it’s manufacturing new smart phones and cars and televisions, or robots and laptops and airplanes. If it turns out to be difficult to bring back old blue collar jobs like those in coal mining or the steel industry, please consider supporting some new jobs based on the strength of the American scientific research enterprise. Start-up companies that create high wage jobs sprout in research parks around healthy university research communities—not just in Silicon Valley or outside Boston but in Indiana and North Dakota and Louisiana and South Carolina. And rebuilding our infrastructure, a goal shared by both Parties, will require lots of innovation, especially for things like power grids, internet access, treatment plants, and efficient transportation systems.

Second, a host of nasty diseases that we don’t have good cures for strike our fellow Americans—diseases like diabetes, congestive heart failure, Alzheimer’s, Parkinson’s, and many cancers. As we all get older, one of these dreadful diseases is likely to catch up to you and me and many of our family members. (I’d be remiss not to mention that others—like malaria, TB, respiratory and diarrheal diseases, AIDS—hit hard in much of the rest of the world, but perhaps we can save this discussion for another time.) If you ask the CEOs of our big pharmaceutical companies, I expect they’ll tell you that their companies’ successes depend on the basic research carried out by members of my professional society and other similar ones. It may surprise you to learn that many of the genes implicated in human disease were first discovered in organisms like fruit flies and roundworms and baker’s yeast. I should mention, too, that the pharmaceutical industry hires the scientists and engineers trained in our university labs. It’s simply good business practice to bolster support for basic research.

Third—and here’s where I hate to get into disagreement with you—but please hear me out: The world really is warming up and humans really are to blame. Don’t take my word for it; I’m no climatologist. Talk to residents in some coastal communities of states like Florida and Georgia and ask them about the tidal flooding that’s already happening. Look at the open letter that BP, Shell and other oil companies wrote to the UN last year that said, “Climate change is a critical challenge for our world.” Ask the heads of our major energy companies—preferably in a quiet White House setting away from the glare of the media and Congressional members of your party—whether they are worried about climate change, like the 2/3 of Americans who took a Gallup survey earlier this year. New sources of clean energy could fuel a lot of new jobs that might otherwise land in China. And while neither of us may be the most religious of men, Genesis tells us that man was put in the Garden of Eden “to work it and keep it” (“keep” here can also be translated as “guard” or “protect”)—a biblical injunction to take care of the environment that many fellow citizens, including a large number who voted for you, take seriously.

I could go on with topics like these, but surely you’re aware that your administration could become badly tripped up by a wholly unforeseen crisis whose causes and solutions may be addressable by science and technology: a global pandemic spread by a drug-resistant pathogen, for example; or disease-carrying mosquitos colonizing large swaths of our country; or a giant oil spill burning out of control; or a furious superstorm exacerbated by rising sea levels. As a businessman, you must appreciate that it’s only prudent to find real scientific experts who can assess these kinds of risks and help you plan for contingencies.

If you want to bring America together, a great way to start is by declaring your respect for science, and by persuading those who deny the results of scientific enquiry to re-examine the evidence. From one president to a soon-to-be other, please consider it.

 

Respectfully,

Stan Fields

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That which we call AROSE https://genestogenomes.org/that-which-we-call-arose/ https://genestogenomes.org/that-which-we-call-arose/#comments Tue, 01 Nov 2016 12:00:06 +0000 https://genestogenomes.org/?p=7590 I’m a total sucker for new methods. I couldn’t wait to try out Trans-Helical Illumination (THI), in which low intensity lasers prime conversion of helical proteins. The potential of Synthetically Integrative Sensor Neurons (SISN) to probe brain subregion function is inspiring. Closer to my own heart, we have high hopes that Optical Wavelength Assembly of…]]>

Frameshifts LogoI’m a total sucker for new methods. I couldn’t wait to try out Trans-Helical Illumination (THI), in which low intensity lasers prime conversion of helical proteins. The potential of Synthetically Integrative Sensor Neurons (SISN) to probe brain subregion function is inspiring. Closer to my own heart, we have high hopes that Optical Wavelength Assembly of Yeast Tetrads (OWAYT) will solve a persistent roadblock with this wonderful fungus. In a similar vein, my mass spec buddies have been raving about how On-gel Exchange of Cross-linked Proteins (OEXP) should get around one of their longstanding problems.

The genetics of differentiation will surely never be the same now that Loci Association in Nascent Stem Cells (LAINSC) has been developed. Some of our most complex data make sense only after we apply the Interconnected and Extended Networks (IEN) algorithm. Finally, even the hottest of fields is being revolutionized by Cluster-independent Editing (CE). And all this, just in the last month.

acronym cartoon

 

I got so jazzed by these new approaches that the lab planned out a few experiments to capitalize on all of them at once. Although LAINSC didn’t give us the resolution we had hoped for, we could correct its errors using CE with IEN analysis. But when we applied THI in tandem with OEXP to SISN, the data were unfortunately just gobbledygook. And we never did get OWAYT to work as advertised.

When I glanced at my online notebook page detailing our efforts with these methods, I was stunned to reread my subject line where I had typed their names all in a row: THI SISN OWAYT OEXP LAINSC IEN CE.

You may not be too surprised to learn that I detest acronyms, especially acronyms for methods. It usually takes reading only to the second paragraph—where a novel acronym first gets used without its long-winded original name—to get me totally lost, because I don’t have a prayer of remembering what the acronym stands for.

Creative acronymologists must surely believe that we keep their strained collection of juxtaposed terms (or, as we call it, their SCJT—pronounced “skajit”) ever present in our minds. Fat chance. They might do better to call their methods John, Paul, George and Ringo—the members of a rock group known popularly in the 1960s and 1970s as The JoPaGeRis (pronounced “joe-pah-jerries”)—for all that their acronyms resonate with most biologists.

Consider one of the most famous methods in molecular biology, published by Fred Sanger and colleagues in 1977 in the Proc. Natl. Acad. Sci. U.S.A. Sanger refers throughout this paper to “the method” or “the current method” or a “new method” but never christens it with a name more catchy than the “inhibitor method.”

In time, the technique came to be called “dideoxy sequencing” or “Sanger sequencing” (but never—whew!—as di-seq or Sang-seq). Dideoxy sequencing—a name good enough for the method that won a second Nobel Prize for Sanger—should serve as the quintessence of naming. It is brief, descriptive and utterly characteristic; no one confuses the term with any other method, fails to appreciate how the method works, or forgets the words behind some bizarre and cute acronym that bears little connection to the original name.

My plea to methods developers and anyone else who comes up with a hitherto unnamed technology, macromolecule, database, cell, theory, or any other object is simple. Unless you can guarantee that your new object will become as well known as PCR, spare us the acronym and provide instead a short name that captures its essential qualities. If that doesn’t work, go with Ringo.

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Something in common https://genestogenomes.org/something-in-common/ https://genestogenomes.org/something-in-common/#comments Mon, 17 Oct 2016 12:00:53 +0000 https://genestogenomes.org/?p=7470 According to a survey from the Pew Research Center, 33% of Americans believe that God created humans in their present form within the last 10,000 years and another 24% believe that God guided evolution over millions of years to create humans as they exist today. While scientists should respect people’s deeply held religious beliefs, it…]]>

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According to a survey from the Pew Research Center, 33% of Americans believe that God created humans in their present form within the last 10,000 years and another 24% believe that God guided evolution over millions of years to create humans as they exist today. While scientists should respect people’s deeply held religious beliefs, it is disconcerting that so many of our fellow citizens are not convinced by the evidence—nearly universally accepted by biologists—that organisms (including humans) evolve through natural selection acting on random variation. I’m working on an explanation of evolution that some evolution doubters may be willing to consider.

Does belief in evolution even matter? Even in a world so dependent on science and technology, is it an issue that much of our populace does not accept the scientific arguments for so fundamental a process?

I think it does matter and it is an issue. The reluctance to accept the reality of evolution erodes support for scientific evidence as a whole, leads to a failure to understand phenomena like antibiotic resistance, cancer progression, and vaccination, and results in a personal sense of blame for diseases or genetic syndromes that arise from the occasional mistakes of DNA replication. The unwillingness of a large fraction of our society to acknowledge well-established scientific truths belies our standing as a technologically advanced nation and endangers our future progress.

evolution

Regardless of their belief in evolution, though, many of our fellow citizens readily provide DNA samples to commercial services that genotype a large number of their genetic markers. From the resulting data, a DNA donor may learn that she is, say, 1/2 Irish; 1/4 German; and 1/16 Norwegian. How do we know this?

To geneticists, the reasoning is simple. Two siblings share 1/2 their DNA because they have the same common—and recent—ancestors, their mom and pop. Each parent supplies a child with one chromosome from each of a set of 23 matching pairs. Because recombination has scrambled the DNA of the chromosomes in the eggs and sperm of their parents, siblings don’t get the exact same fragments of their parents’ chromosomes, and so on average they share only 1/2 their DNA.

First cousins share about 1/8 of their DNA because they, too, have some of the same common—and recent—ancestors, but in this case it’s only one of their two sets of grandparents. So while you share 1/4 of your DNA with each of your grandparents, with your first cousins it’s half of that.

Second cousins share only 1/32 of their DNA because their common ancestor is a set of great-grandparents. And so on. The child of unrelated partners brings two distinct genetic lineages together. As you go back and trace the DNA of more and more distant cousins, you’ll see that they share fewer common ancestors, and recombination each generation continued to scramble up chromosomes.

DNA testing services can identify fourth cousins who share about 1/500 of their DNA and perhaps fifth cousins who share about 1/2000. You’re happy when these distant relatives show up, because while they may not look a whole lot like you, they represent other descendants of one of your long-ago ancestors. If that ancestor happened to live in Norway—which we know because modern day Norwegians have many of the same DNA markers as those who lived there long ago—you have an explanation for why you are said to be a small fraction Norwegian.

Now imagine you provide a DNA sample to one of these testing companies, but imagine, too, that the detection of tiny haplotype blocks that indicate identity by descent has gotten really really good. The company genotypes your markers and finds that you have a match with someone who is your thousandth cousin, because she shares 1/22001 of your DNA. The common ancestor of you and this distant cousin lived about 20,000 years ago.

The testing company pushes the technology even further and comes up with someone who is your ten thousandth cousin; your common ancestor with him lived about 200,000 years ago, just as anatomically modern humans first came on the scene.

But you’re still not satisfied and demand even more distant relatives. So you get back a match with Individual O, who is your 300,000th cousin; you share a common ancestor but that ancestor lived about 6 million years ago. You’re excited to meet this new relative, so the company takes you to a local zoo and introduces you to Individual O, who happens to be an orangutan.

Soon you get an email message that yet another relative has been located through a match with a DNA donor. This Individual D, who is your 4,500,000th cousin, shared an ancestor with you about 90 million years ago. Amazingly, D lives with you and your family and is 100% German, as in German shepherd: you took him for a walk just a few hours ago.

 

 

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No “two cultures” here: send us your art https://genestogenomes.org/no-two-cultures-here-send-us-your-art/ https://genestogenomes.org/no-two-cultures-here-send-us-your-art/#comments Mon, 03 Oct 2016 12:00:45 +0000 https://genestogenomes.org/?p=7293 I’m fond of saying that while scientists often have a hankering to draw sketches, pen novels, compose songs, or carry out other acts of artistic creation in what available free time they have, you don’t find many creative artists hankering to borrow a bit of lab space for a few nighttime experiments. If you’re a…]]>

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I’m fond of saying that while scientists often have a hankering to draw sketches, pen novels, compose songs, or carry out other acts of artistic creation in what available free time they have, you don’t find many creative artists hankering to borrow a bit of lab space for a few nighttime experiments. If you’re a scientist, the GSA would like to see some of the products of your creativity.

However, when I’ve shared this observation about scientists and artists with my wife—who has creative talents and hasn’t worked in a lab since high school chemistry—she bristles and tells me that I don’t know what I’m talking about. She points out first, that I don’t know enough professional artists to have even a clue as to what they do or don’t do in their spare time; second, that many creative occupations—from weaving a textile to cooking a complex dish; from sculpting a figure to knitting a sweater; from sketching a body to imagining a building—require consistent application of quantitative principles; and third, that scientists, of whom she knows more than a few, are no more well-rounded than anybody else. She’s no doubt right on all counts, although I don’t know that this has inhibited me from continuing to hold my misbegotten belief. Chalk it up to the Pghded locus on the Y chromosome.

 

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But since most of you reading this are more likely to be scientists than artists, I’m guessing that you have a fair amount of pent-up creative energy, rather than pent-up experimental approaches that your day job as a filmmaker doesn’t allow you to exercise. The GSA would love to populate our blog with your creativity!

My request is for you to send us stuff: short (fewer than 500 words) stories, poems, haikus, spoofs or whatever else you’ve written or would like to write within this limit; cartoons, sketches or other drawings; artistic photos or photos of your artistic efforts—be they directed toward furniture-, pottery- or jewelry-making, fiber arts, woodworking or any other craft; short audios or videos of you singing, dancing, playing a musical piece you composed, performing a skit; or any other evidence of your unbridled creativity. We will look at all contributions (feel free to send more than one) and post as many examples as we can on this blog. You don’t have to be a GSA member to contribute—but we’d certainly be delighted to learn that you are one!

My fear is that rather than the thousands of artistic efforts I’d hope to see, we will get only three items sent to us, with one of these from someone now in my lab and another from a former postdoc in the lab. This outcome will ensue not because you’re not creative, but rather that you don’t believe your output is worthy of sharing or worth the minimal effort to forward on to us. Of course, it could be, too, that almost no one reads these posts, in which case if you’re the rare reader we need your contribution all the more. And after posting it to us, forward this link on to your friends with known artistic talents and push them to contribute. We’re looking to create a stunning site that showcases the other creative side of geneticists.


To submit your art, please email GenesToGenomes@genetics-gsa.org with “GSA-Art” in the subject line. Include your name, affiliation, some examples of the art you would like to submit, along with a brief description, and we will be in touch with further instructions.

 

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Not IF, we can help it https://genestogenomes.org/not-if-we-can-help-it/ https://genestogenomes.org/not-if-we-can-help-it/#comments Fri, 16 Sep 2016 12:00:52 +0000 https://genestogenomes.org/?p=7196 Perhaps no topic has had more ink spilled by biobloggers – especially if you include electrons dripping out of laptops – than the tyranny of the Journal Impact Factor. A metric designed by Eugene Garfield to help librarians select journals, the IF has been routinely abused for purposes never intended. How can we reverse this…]]>

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Perhaps no topic has had more ink spilled by biobloggers – especially if you include electrons dripping out of laptops – than the tyranny of the Journal Impact Factor. A metric designed by Eugene Garfield to help librarians select journals, the IF has been routinely abused for purposes never intended. How can we reverse this process and reclaim the literature for those who publish research, evaluate research for hiring and tenure decisions, or fund research?

The wrongful uses and misunderstandings of the IF are legion. A measure of a journal’s overall citation rate, it is commonly misapplied to individual articles or—even worse—to the individual authors of those articles. The IF can be heavily influenced by even a single highly cited article, which can push a journal into an impact realm where it doesn’t belong; other sides of this bias are that most articles in a journal accrue considerably fewer citations than the IF would suggest and a small fraction of articles attract the bulk of a journal’s citations. Journals can manipulate their IF. For example, publishing more reviews tends to increase it. And the IF with its three decimal places gives an unwarranted impression of accuracy. Citation patterns are heavily influenced by discipline; more researchers, for example, cite work on cancer than on Chlamydomonas.

 

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My favorite confusion of the IF comes from Eugene Garfield himself. He writes, “of 38 million items cited from 1900-2005, only 0.5% were cited more than 200 times. Half were not cited at all…”. Think about that for a second: half of the cited items over a 105 year period were not cited.

So why does nearly every grad student and postdoc – not to mention a lot of PIs – seek to publish in journals with the highest IF? And given that the majority of journals with the loftiest scores are edited by professional rather than academic editors, why do we relinquish so much of our evaluative responsibility to those with some of the least experience in doing science? Why do we sustain the vicious cycle that results when we send our best work to journals with highest IFs, which allows them to maintain their standing, which leads people evaluating scientists to use journal names as a proxy for the quality of research?

I have heard only one rationale for this situation that makes sense, albeit twisted sense: any postdoc who has persisted through the entire process—the convince-the-editor-to allow-the-manuscript-to-go-out-to-review process, the argue-with-the-editor-that-the-negative-review-is-not-relevant process, the rally-the-troops-to-get-the-work-done-for-the-revision process, the wear-down-reviewers-and-editor-in-the-endgame process—to wind up with a publication in one of the famed one-word journals shows the grit and guts necessary to succeed as a faculty member, regardless of whether or not their publication makes a valued contribution.

Tame measures have been proposed for replacing a lame measure with the same sort of measure: instead of IF, let’s use a score based on how often an individual article is cited; or a score based on how an author’s n papers have been cited at least n times; or a score based on how often each journal cites each other; or some other complex score. My favorite alternative is that we give jobs and grants and tenure to those scientists whose articles have created the most internet buzz, as scored by a decibel meter. While any of these (save perhaps the last) might be a marginal improvement, they hardly solve the problem.

The simplest solution is that those who evaluate science simply read the papers of those being evaluated and make their own decisions about the quality and significance of the work. Search committees might dodge this obligation by pleading they have too many applicants. Study section members get less of a pass because they are reviewers of a limited number of grant applications. Those asked to comment on the suitability of a candidate for tenure get no dispensation for ignoring the content of the publications of the one person they are asked to consider. But I fear that those who would avoid reading the literature will avoid reading the literature. Now what?

I propose a two-part solution: half standard, half structural. The standard: instead of providing the usual CV that lists all publications, biologists should be allowed to list only a very few, perhaps five. For each, they provide a summary of why the research is significant, how it advanced its field, how it was not duplicated by the work of others, and what their specific role in the work was. The structural: they list each publication only by article title and authors, and leave off the journal name, volume and page numbers. In fact, the NIH could readily put a crimp into the IF by simply not allowing journal names to appear in the biosketches of grant applicants; universities could follow suit by not allowing journal names in the CVs of job or tenure candidates.

Of course, this no-names policy might be circumvented by a reviewer who insists on searching out the missing journal names. But perhaps the reviewer was already seduced by the persuasiveness of an author summary to give the applicant a second look, even to the point of reading an article (provided, of course, in manuscript format without obvious journal affiliation). Maybe other committees circumvent the policy by hiring an underling to do a PubMed search to ferret out the journal names of every article in every CV submitted. If that occurs, then PubMed won’t be allowed to list journal names. If this is still insufficient to ensure journal anonymity, then the journals won’t be allowed to use their names; each will be identified by the sum of the digits in its IF times a random number, which will change daily.

In the end, the only criterion of significance is the work itself, and we all know lots of significant work that appeared in multi-word journals and the converse for single-word journals. If we can’t figure this out without IF figures, then we deserve the wrong faculty we hire, the wrong faculty we fund, and the wrong faculty we tenure. The next time someone tells you that a biologist must be talented because she published in [one-word journal] and [another one-word journal], say that you read those papers and they were garbage (don’t worry if they happened to be exceptional). If we all say this enough times, maybe we’ll get our colleagues to refer to the research rather than its unjustified proxy.

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An executive decision https://genestogenomes.org/an-executive-decision/ https://genestogenomes.org/an-executive-decision/#comments Wed, 31 Aug 2016 18:59:51 +0000 https://genestogenomes.org/?p=7153 I am pleased to announce the appointment of Tracey DePellegrin as the new Executive Director of the GSA. Tracey has been the Executive Editor of our two journals, GENETICS and G3. Those of you who have not been president of the GSA—a population that included me until this year—may well be asking, “What does an…]]>

Frameshifts LogoI am pleased to announce the appointment of Tracey DePellegrin as the new Executive Director of the GSA. Tracey has been the Executive Editor of our two journals, GENETICS and G3. Those of you who have not been president of the GSA—a population that included me until this year—may well be asking, “What does an executive director of a scientific society do?” But even if you don’t know the job description, I seriously doubt that any of you who have interacted with the GSA journals—as an author, reviewer or editor—is asking, “Why Tracey?”

The answer to the first question, about the job of our Executive Director, is simple: The Executive Director does a lot. She is the chief administrative officer of the Society, responsible for programs and policies that include the journals, conferences, communications, trainee professional development, education and advocacy. The Executive Director manages our staff, oversees our financial operations and develops new programs and initiatives in conjunction with the GSA Board of Directors. In short, unlike the volunteer academic leadership of the Society who wash up on the GSA shore with the trade winds of each election cycle, the Executive Director is a full-time professional providing the fixed marina where the yearly academic flotsam and jetsam come to rest.

Tracey2The answer to the second question—why the Board of Directors chose Tracey—is also simple: She is the ideal person to lead the GSA during a time when scientific societies face a difficult and complex transition. Access to a journal like GENETICS, long a major reason to join a society, is free to most academic users. And the traditional loyalties of our profession that made it standard to join the society that best represented one’s science no longer hold much sway with many young geneticists. We need to have an executive director with enthusiasm and energy, good people skills, diplomacy, a substantial track record of successful management and mentoring, and the ability to navigate the ever-changing challenges faced by our members and communities. Tracey brings all these traits, along with a deep knowledge of and commitment to our Society, having been on our journal staff since 2003.

Tracey has an outstanding track record leading our editorial office and journal teams. She strengthened journal finances and managed GENETICS’ transition to be online only. She helped the editors expand the content of GENETICS, implementing new article types such as the model organism “Book” series, Commentaries and Toolbox Reviews. She implemented innovative features like the linking of genetic terms in papers to the model organism databases. Tracey spearheaded the launch of our open-access journal G3 in 2011, and ushered its growth to ~40 papers every month. And she launched a new website for GENETICS in its 100th anniversary year. Both journals have gained in visibility and have developed a well-earned reputation for fairness, for speed, and for tackling thorny editorial and publication issues. She oversaw the launch of our Genes to Genomes blog (which you’re reading now), and initiated the use of social media to highlight articles in our journals. She began a science writing internship program, which has hired grad students and mentored them in writing skills (one of their posts is the most viewed post ever on the blog). She’s made it a priority to ensure that authors, editors, and reviewers experience a highly-responsive, cohesive editorial office where concerns are addressed as rapidly as possible. A measure of Tracey’s stature within her own community is her appointment as Editor-in-Chief of Science Editor, the journal for the Council of Science Editors.

Tracey and the Society’s journal team are based in Pittsburgh, and will continue there with this change in Tracey’s title. In consequence, the GSA will continue to have operations both in Bethesda and in Pittsburgh, but its center of gravity will move a bit west. While this reduces some of our presence in the D.C.-based scientific power structure of the NIH, the NSF, Congressional staffers and our many other sister societies, it lets us stay nimble and seize opportunities that can arise when issues can be approached with more of an outsider’s perspective. Those of you who have lived in or visited Pittsburgh know that the city is attractive and vibrant, with two major universities and strong biomedical research (even if some of us who live in Seattle are a little less excited about its football team).

The GSA is 85 years old, but should you be getting out the cane and walker for us? Not happening. Some of our best ideas lie ahead of us, and I’m glad that Tracey has signed on to help develop and implement them. Please join me in welcoming Tracey to this leadership position.

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