Tyson’s Advice for Students

Production note: 
correction to the subtitles on the video: “Resighted” = “Recited” (spelling error)

lots of earlier mistakes getting caught in the ray fin fish clade which continues to be under scrutiny (e.g. see yesterday’s post on swordfish). Hope to have all wrinkles ironed out soon. Thank you for your patience. The LRT is an ongoing hypothesis of interrelations subject to change with more data and more understanding.

And a Bonus Video from Joe Rogan featuring Avi Loeb


Roundtable discussion on YouTube: How to be a scientist

I quote-mined the round table video conversation below.

  1. Host Carl Zimmer, author
  2. Panelist Mariette DiChristina, editor-in-chief, Scientific American
  3. Panelist Dany Spencer Adams, developmental biologist
  4. Panelist Ivan Oransky, journalist
  5. Panellist Massimo Pigliucci, biologist, philosopher

Video caption:
“As a discipline, science aspires to be an evidence-based, non-partisan tool for revealing truth. But science is carried out by scientists, human beings like the rest of us, subject to pressures, preconceptions, and biases. What are the external, non-scientific forces that impact scientific research? Does the current research structure drive focus away from unbiased exploration? What lessons can we draw from the recent crisis of reproducibility afflicting some research areas? In this program, experts discuss the myriad factors scientists face in a highly competitive environment as they seek to uphold and advance the ideals of scientific exploration.”

According to Massimo Pigliucci:

  1. “Write your materials and methods first, then your results, then your introduction last.”
  2. “Overcome confirmation bias. What if your result is something that is not predicted?”
  3. “There’s no incentive to replicate someone else’s results. You want to be the first one to get there. Not the second one. Most journals, especially the high-impact journals want the novel stuff, the sexy stuff, the stuff that nobody’s done before. [Even so…] Two-thirds of papers in top journals never get cited within five years. 
  4. “There are 150 applicants for every paid position.” 
  5. Some scientists want to see and approve pre-published stories, to check their quotes. 
  6. Blogposts represent the direct voice of the scientist. Historically this has been a problem because you’re wasting your time, andyou’re not including other scientists. 

According to Dany Spencer Adams:

  1. “Science is one way of learning things.”
  2. “If you’re not failing most of the time, you’re not working hard enough.”
  3. “Don’t send anything from a Mac to a PC. Don’t update your software within a week of your deadline. Formatting to a journal’s style takes time. Reformatting from one journal to another (after the first rejection) takes more time.”
  4. “Only the top 4 percent of applications receive funding from the NSF.” 

According to Ivan Oransky:

  1. “Ask yourself, How can I prove myself wrong?”
  2. “If a paper is published and no one cites it, does it really matter? So getting published in high-impact journals is important in Academia.”
  3. The number of retractions (from fraudulent data collection or misconduct) has dramatically increased, but remains relatively rare. Current record holder: 183 retractions from a single individual. Falsification, Fabrication and Plagiarism: the Triad. Some authors were caught doing there own peer-review, or each others’ peer-reviews in cooperation. His ‘Doing the Right Thing Award’ is given to those who make corrections at some cost to themselves.”

According to Carl Zimmer:

  1. “Much time is spent filling out paperwork to get grants.”
  2. “Are journalists part of the problem?” 

According to Mariette DiChristina:

  1. “Science tries to embrace corrections.
  2. “Materials and methods should produce replicable results.
  3. “Many of us are click-bait chasers. Invite the researcher to tell the story of how the results came to be, describe the human endeavor. Provide the context.”

In the old days:
scientists simply wrote their papers without grants, without referees, without competing for journal pages, without waiting for months or years for all this to take place. There were far fewer scientists working back then, and there was more ‘low-hanging fruit’ waiting to be plucked (= discovered). Then again, new ideas were still ridiculed until confirmed.

scientists produce blogposts, send unpublished, unrefereeed PDFs to ResearchGate.org and write books. Others publish without referees, competing for grants, dealing with students, dealing with administrators, principal investigators or all of the above. Some scientists making contributions are not PhDs.

Readers should gather by now
that sometimes scientists make mistakes, often by the sin of omission (= taxon exclusion) and due to that, they sometimes come to improper conclusions. This happened in the past and it continues to happen in the present. When I make mistakes I correct them. It’s part of the learning process. If nothing else, I hope that readers will take from this blog the idea that all hypotheses should be questioned and all conclusions should be tested. It’s okay to do this, no matter how many PhDs are listed as co-authors. Tradition can be wrong. Sometimes people will despise you for upsetting favorite traditions. A long list of well-known scientists have been despised for their views, hypotheses and theories.

Don’t wait.
The ‘low-hanging fruit’ is quickly disappearing with every new discovery. This is a golden era in paleontology that will someday dry up as questions are answered and topologies are cemented.

Side note:
Panelist Mariette DiChristina was the online editor-in-chief at Scientific American where Dr. Darren Naish published his Tetrapod Zoology blogpost for several years. Recently they parted ways and Dr. Naish has reported a new interest in non-tetrapod vertebrates (= fish).

I’d like to see Dr. Naish continue his interest in tetrapods, perhaps to ultimately create a wide gamut cladogram of tetrapods and compare it to the results recovered by the large reptile tree at ReptileEvolution.com, which he continues to disparage. Let’s all hope Dr. Naish is not a subscriber to Massimo Pigliucci’s statement #3 (above). To that point, as everyone knows, in EVERY CASE I am ‘the second one’ to describe a taxon. Even so, and as proven here, there are still a good number of discoveries to be made out there.

Last minute addition:
Dr. Steve Brusatte how new discoveries are presented in the press.

E. O. Wilson: Advice for young scientists

Readers of this blogpost will appreciate
what the ‘Ant Man’ E. O. Wilson has to say to budding scientists. Click the image to play.

Wilson’s principles:

  1. Find a field which interests you deeply and focus on that.
  2. A certain level of a subject (e.g. mathematics) is already enough to achieve excellence.
  3. March away from the sound of the guns. (don’t enter the fray, create your own fray)
  4. The more difficult the problem; the greater will be the importance of the solution

One of the responders wrote:
“One thing I would say to any scientist – including young scientists – is to avoid dogma. Scientists these days are guilty of things that they sometimes accuse religious people of, and that is making speculations and passing them as fact. If you have a hypothesis or claim, prove it! Write a paper detailing your methodology, describe your results and put forward your conclusion. Then let the reader come to his or her own conclusion whether your hypothesis has any merit.”

The First Anniversary of ReptileEvolution.com – Dec 21

December 21 marks the first year anniversary of ReptileEvolution.com, the basis and chief reference for the PterosaurHeresies.comReptileEvolution.com was created to get the word out on the various mistakes and oversights in the current literature. These errors were found principally by testing them against the relationships recovered from the large reptile family tree. Some morphological insights were also reported. Proper nestings and great papers were given all due honor.

Frustration, the Mother of all Invention
As mentioned on the “About” page, the impetus for the creation of ReptileEvolution.com came about after getting one last manuscript rejected at the hands of various pterosaur experts who did not want my work to make it into the literature. Yes, my work opposed theirs and suppression was their motive. Sadly, they continue to prefer untenable nestings and bizarre descriptions.

Turned Out to Be a Good Thing!
Had those manuscripts been accepted, the published papers would have languished in quiet isolation on college library shelves, like most papers do. Now the data and results enjoy free worldwide exposure and access. Rather than standard black and white printed imagery, the web permits full color with video overlays and animation. The speed of reporting has been accelerated. Here, updates, additions and corrections take less than a day.

The Tree Keep Growing
A year ago
the reptile tree stood at some 230 taxa, not counting the pterosaur tree, which stood at 165 or so taxa. Today the reptile tree includes 279 taxa, the pterosaur tree includes 180 taxa and the basal therapsid tree includes 39 taxa for rough total of about 500 taxa, give or take some overlap and estimating as I write this 2 weeks prior to uploading. All trees are resolved with high Bremer Test scores. I’m pleased to report that workers are requesting the data matrix for their own studies.

The structure of the tree has not changed so far, despite the influx of 20% more taxa. That’s a good test. Certain taxa have shifted a node or two. That happened as I found mistakes in the matrix that were corrected while uploading new taxa. Correcting mistakes and oversights is the process of science.

The Insights Have Been Very Rewarding
The results speak for themselves. The feedback has been gratifying. The process has been more than interesting. Nothing beats making a discovery!

Thank you for following this blog and checking out the data presented in ReptileEvolution.com. I value your input and will continue to modify any statements and images that are not right on the mark.

Here’s to a great future in prehistory!

Best regards,
David Peters

re: Traps for Journalists to Avoid

A recent blog by Dr. David Hone entitled Traps for Journalists to Avoid brought up some interesting and valid points. His “tell-tale warning signs” provided some important topics that are worthy of consideration — and others that need to be tempered with an opposing thought or two.

Dr. Hone requested journalist to question their sources, by asking themselves, Is there actually a proper paper? If this story is coming from a conference abstract, grant proposal, self-published manuscript, website etc. then simply leave it be. If this thing cannot get past peer review, or has not tried, it’s not even passed the most basic test of the scientific process. You’re simply asking to be taken in by a nutty idea that has simply slipped, unreviewed, into a conference (and quite possibly sneakily – the content to a talk can be quite different to the title). If there is at least a proper paper in a proper journal that’s a good start.

That’s good advice, generally, but perhaps a bit overstated. Unfortunately, as this blog, The Pterosaur Heresies, have reported time and again, even peer-reviewed published papers sometimes fail to provide valid results. Rather a few promote “nutty ideas.” That’s because everyone has their own little blinders on. Let’s face it, we all suffer from human prejudices and paradigms that push away opposing data. We see what we want to see. Sometimes (hopefully rarely) this occurs in clades of scientists, Their papers get approved by collaborators who also follow bad paradigms, bow to politics, or what have you*. Ideally a manuscript should be sent to one’s harshest critics. Through the hate and vile some truth may appear in those red ink comments. However, the raw emotion and pure negativity can also mask a lack of good opposing evidence. If that’s the case, then a scientist has to move forward. Scientists generally don’t like to have their pet hypotheses “stepped on,” but sometimes that just has to happen…somehow…as a last resort on the web, if all other venues are blocked.

It is not the job of journalists to judge or test published works.
That is the job of other scientists. So how can scientists in the far corners of this planet become aware of novel hypotheses and discoveries unless they are somehow published or promoted? When opposing evidence is prevented from academic publication because the manuscript results overturn the referees’ own hypotheses, then we have something akin to conflict of interest. That happens more than most people realize because its a small world of referees. The ones that are most opposed to certain hypotheses are the ones that are more than happy to referee those manuscripts, to make sure they never get published. Certainly some papers are premature and poorly supported. However, when opposing arguments are inappropriately blackballed then science suffers.

Only when third party scientists are able to test one hypothesis (medicine, method, observation, etc.) against another do we get closer to the truth. So, the basic test of the scientific process is not getting past peer review, as Dr. Hone said. The basic test of the scientific process is to test, test and test again and this can only happen with a free flow of widely available information. Then, whatever made a good paper a century ago or a week ago can quickly become a bad paper when tested against a larger data set or more precise observations. The good papers will float. The bad ones will sink over time.

Dr. Hone also warned against “really odd” results and hypotheses. His solution, “Ask around. And try to avoid regular collaborators of the person in question – their friends might well support them. But if you keep hearing “he said that? really?” then be careful. This might have got through peer-review but no-one seriously buys it.” 

Science Is Not a Popularity Contest
Unfortunately, Dr. Hone is arguing for immediate popular approval, which no novel hypothesis has ever overcome (without the benefit of the passage of time). Everything from feathers on dinosaurs to continental drift has suffered, at first, from their own audacious novelty. The expert are STILL holding on to “pterosaurs are archosaurs,” “wing membranes attach to the ankles,” “modular evolution” and nearly every other “nutty idea” argued against in this blog.

You can’t introduce a discovery without pissing someone else off. Importantly, this “Loyal Opposition” is a good thing IF the arguments and observations are valid. Defending a novel theory is also a good thing. These opposing hypotheses have to be published so this back and forth conversation can begin. Scientists need to be able to put all their cards on the table to see who folds for lack of evidence and support. This may sometimes take more than a lifetime.

There are some paradigms and traditions that just need a good dusting. Others need to be tossed out. When novel hypotheses are newsworthy hopefully journalists will be there to promote them so other scientists have the opportunity to test, test and test again.

*The most common problem I’ve seen is the continuing reliance on small gamut untested inclusion sets in cladistic analysis, a situation remedied here with a large gamut inclusion set.

Your comments are welcome.