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In 'Guardians of the Galaxy Vol. 2,' Planet Sovereign Defies Physics

Wired Science - 7 hours 17 min ago
Is there a physical reason why a planet might have ended up looking like some sort of fat, intergalactic caterpillar?
Categories: Bio

Offensive overselling of the #microbiome in breast cancer from the Cleveland Clinic

The tree of life - 10 hours 1 min ago




This is just sickening to me.

I saw a news story that smelled funny:  Breast cancer: Bacterial deficiency linked with onset. And I went and found the scientific paper and then the press release from the Cleveland Clinic that the news story seemed based on.  And, well, the press release turns out to be ridiculous.

The paper showed something somewhat interesting but very limited.  Here is the abstract with key parts bolded and underlined by me
It has long been proposed that the gut microbiome contributes to breast carcinogenesis by modifying systemic estrogen levels. This is often cited as a possible mechanism linking breast cancer and high-fat, low-fiber diets as well as antibiotic exposure, associations previously identified in population-based studies. More recently, a distinct microbiome has been identified within breast milk and tissue, but few studies have characterized differences in the breast tissue microbiota of patients with and without cancer, and none have investigated distant body-site microbiomes outside of the gut. We hypothesize that cancerous breast tissue is associated with a microbiomic profile distinct from that of benign breast tissue, and that microbiomes of more distant sites, the oral cavity and urinary tract, will reflect dysbiosis as well. Fifty-seven women with invasive breast cancer undergoing mastectomy and 21 healthy women undergoing cosmetic breast surgery were enrolled. The bacterial 16S rRNA gene was amplified from urine, oral rinse and surgically collected breast tissue, sequenced, and processed through a QIIME-based bioinformatics pipeline. Cancer patient breast tissue microbiomes clustered significantly differently from non-cancer patients (p=0.03), largely driven by decreased relative abundance of Methylobacterium in cancer patients (median 0.10 vs. 0.24, p=0.03). There were no significant differences in oral rinse samples. Differences in urinary microbiomes were largely explained by menopausal status, with peri/postmenopausal women showing decreased levels of Lactobacillus. Independent of menopausal status, however, cancer patients had increased levels of gram-positive organisms including Corynebacterium (p<0.01), Staphylococcus (p=0.02), Actinomyces (p<0.01), and Propionibacteriaceae (p<0.01). Our observations suggest that the local breast microbiota differ in patients with and without breast cancer. Cancer patient urinary microbiomes were characterized by increased levels of gram-positive organisms in this study, but need to be further studied in larger cohorts.
That is it.  Barely significant finding of some clustering of the microbiomes of breast cancer patients versus those of patients without breast cancer.  And yet, this turned in the press release into cancer causing bacteria that they will be fighting with nanotechnology.  Seriously.

The press release title and subtitle is semi OK:
Cleveland Clinic Researchers Find Link Between Bacterial Imbalances and Breast Cancer. Study compares bacterial composition in healthy vs. cancerous breast tissue
But it goes way way way downhill from there.  Here are the parts with problems
  •  In our wildest dreams, we hope we can use microbiomics right before breast cancer forms and then prevent cancer with probiotics or antibiotics
    • Sure, in my wildest dreams I would cure cancer too.  
  • In addition to the Methylobacterium finding, the team discovered that cancer patients’ urine samples had increased levels of gram-positive bacteria, including Staphylococcus and Actinomyces. Further studies are needed to determine the role these organisms may play in breast cancer.
    • Umm.  No. Further studies are needed to see if these organisms play ANY role of any kind in breast cancer.
  • Co-senior author Stephen Grobymer, M.D., said, “If we can target specific pro-cancer bacteria, we may be able to make the environment less hospitable to cancer and enhance existing treatments. Larger studies are needed but this work is a solid first step in better understanding the significant role of bacterial imbalances in breast cancer.
    • Noooooooooooooooooooooooooooo.  You have not shown anywhere that there are "pro cancer" bacteria and this quote clearly implies that you have. 
  • The study provides proof-of-principle evidence to support further research into the creation and utilization of loaded submicroscopic particles (nanoparticles), targeting these pro-cancer bacteria. 
    • What?  This study does not provide ANY proof of principle of this sort.  You have not shown there are any pro-cancer bacteria.  This is ridiculous and offensive.  
No wonder the news stories imply that this study is about preventing breast cancer.  The press release from the Cleveland Clinic is deceptive.  It makes claims about the work that are irresponsible, misleading, and potentially dangerous. The Cleveland Clinic should be ashamed.

And thus the Cleveland Clinic is the winner of this edition of the Overselling the Microbiome Award.


UPDATE 10/16/17

And so the deceptive PR from Cleveland Clinic is now leading to claims of "Antibiotics May Prevent Breast Cancer" See



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This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter.
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Categories: Bio

Nature Publishing Group continues to deceive about #OpenAccess to genome papers

The tree of life - 10 hours 15 min ago
I was reminded today about the wonderful history of Nature in it's claim that it would make all papers reporting a new genome sequence freely and openly available. I wrote about how this was, well, not the truth, in 2012: The Tree of Life: Hey Nature Publishing Group - When are you going to live up to your promises about "free" genome papers? #opengate #aaaaaarrgh. And today I decided to recheck this.

So I searched for "Genome sequence" on the Nature site

And, well, I found a doozy of an example of a paper that is supposed to be openly available but is not. Initial sequencing and analysis of the human genome



That's right.  The "public" human genome paper is not freely or openly available.  It is $4.99 to rent or $20 to purchase.  Is this Nature's way of saying "We think the Lander et al. paper did not actually report on a genome?" and that the Venter paper truly won the race?  I don't think so.  I think this is a way of Nature saying "How can we make money off of our past papers? Which one gets a lot of looks? What? It is freely available? Change that." or something like that.

Want to bet they will say this is a mistake?  Want to bet they will not refund anybody's money who paid for this?

Here is a simple solution for everyone out there.  Do not trust Nature Publishing Group to make something available even if they say they will.


UPDATE 9/25 1 PM

But wait - there is more.  The Plasmodium genome paper, which I wrote about in 2012 not being available and which Nature promised to fix is again behind a pay wall










And more



UPDATE 10/16/17

Nature has apologized and said they fixed the issue and will refund any money people spent to buy these articles




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This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter.
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Categories: Bio

This week in Science SPAM

The tree of life - 13 hours 17 sec ago
I would love it if I could just ignore my Gmail Spam folder.  Alas, every once in a while I find important emails in Gmail Spam.   So alas I cannot ignore it. While digging through today I found a collection of "Science Spam" - that is Spam emails that have some science-y theme.

Here are the ones from this week in my Gmail Spam folder that I identified as being Science Spam.   Most are invites from Spammy journals.  Some are invites from Spammy conferences.  A few are other things.  Do other people get this much science Spam?











































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This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter.
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Categories: Bio

Neutron Stars Collide, and the Gravitational Wave Sends Ripples Through Astrophysics

Wired Science - 13 hours 46 min ago
Scientists detected their fifth gravitational wave in August, and announced it today. But keeping the discoveries quiet is getting harder and harder.
Categories: Bio

Lunar Scientists Want to Hitch a Ride on America's Next Moonshot

Wired Science - 16 hours 46 min ago
At the beginning of the month, Vice President Mike Pence announced that the US, at long last, will go back to the moon. Well ... some day.
Categories: Bio

From Google Scholar: Follow Related Research for Key Authors

The tree of life - Sun, 10/15/2017 - 21:40
This seems like it could be useful:



Google Scholar Blog: Follow Related Research for Key Authors


Scholar provides several ways to keep up with research in your area. You can set up keyword alerts, get recommendations related to your publications and follow your colleagues’ profiles.

Today, we are adding another approach to stay up to date in areas of your interest. Now, in addition to following articles by and citations to an author, you can follow research that is related to her work. 
To follow related research for an author, simply go to her public profile, click “Follow” and select “New articles related to this author’s research”. Scholar will automatically scan all new publications for articles related to her research and will send them to you as an email alert. 
This is particularly useful if you are a graduate student or an early stage researcher. By following related research for your advisor, your thesis committee and possibly a few key faculty members in your department, you would be able to see the research landscape from their experienced vantage point.

It is also useful if, like myself, you are an industry or medical professional who isn’t active in the research realm but would like to keep up. By following related research for leading scholars, you will be able to quickly view relevant articles in key areas.
The astute reader has no doubt guessed that this can also be used to get email alerts for research related to your own work -- go to your public profile, click “Follow” and select “Recommended articles”.


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This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter.
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Categories: Bio

Ultra-Powerful Radio Bursts May Be Getting a Cosmic Boost

Wired Science - Sun, 10/15/2017 - 07:00
Repeating radio bursts are among the most mysterious phenomena in the universe. A new theory explores how some of their puzzling properties can be explained by galactic lenses made of plasma.
Categories: Bio

Nathan Myhrvold's *Modernist Bread* Reveals the Secrets of Gluten

Wired Science - Sat, 10/14/2017 - 07:00
Nathan Myhrvold's second food manifesto, *Modernist Bread*, is a $625, five-volume labor of loaves.
Categories: Bio

How the Napa Fires Could Hurt 2017's Wine Grapes

Wired Science - Fri, 10/13/2017 - 16:08
Smoke from California's fires could make grapes left on the vines taste like ash—if the vines survive at all
Categories: Bio

Meet the Geek Who Tracks Rogue Satellites With Coat Hangers

Wired Science - Fri, 10/13/2017 - 09:00
Since 2012, Mike Coletta has been eavesdropping on the sky, picking up signals from satellites that were never meant for him.
Categories: Bio

The Crowdsourced Maps Guiding Puerto Rico's Recovery

Wired Science - Fri, 10/13/2017 - 08:00
Volunteers across the globe are filling in maps of Puerto Rico. How do humanitarian workers use them?
Categories: Bio

NASA's CO2-Tracking Satellite Deconstructs Earth's Carbon Cycle

Wired Science - Thu, 10/12/2017 - 14:00
Five new studies show how rising temperatures could push the planet's carbon sinks to their limits.
Categories: Bio

Save the date: Annual French C. elegans Meeting

WormBase - Thu, 10/12/2017 - 12:47

The 21st edition of Ver Midi will be held at the CIML, Marseille on Friday 26th January 2018, with Henrik Bringmann as invited speaker. It will be preceded by a workshop on high-throughput methods on the 25th, sponsored by Union Biometrica and TECAN.

The website for registration will open in November.

Please contact the organisers, Nathalie Pujol, Jonathan Ewbank or Vincent Bertrand if you wish to be added to the Ver Midi mailing list.

Categories: Bio

You Aren't Ready for the Weirdness of Working With Robots

Wired Science - Thu, 10/12/2017 - 08:00
Welcome to the world of human-robot interaction, in which people have to adapt to the machines as much as the machines have to adapt to us.
Categories: Bio

In the Wake of the Santa Rosa Fire, It's the Smoke, Not the Fire, That Will Get You

Wired Science - Thu, 10/12/2017 - 07:00
In these urban smoke islands, it's harder to get away from the air-borne particles that can wreak havoc on your health.
Categories: Bio

Could Spider-Man Actually Pass Physics?

Wired Science - Wed, 10/11/2017 - 10:00
Turns out, superheroes don't just illustrate physics—they *do* physics, too!
Categories: Bio

Inside Cells, Genetic War Could Create New Species

Wired Science - Wed, 10/11/2017 - 09:00
Mitonuclear conflict—a struggle between the genes in a cell’s nucleus and those in its mitochondria—might sometimes split species in two.
Categories: Bio

The Fires in Napa, Sonoma, and Santa Rosa Are a Perfectly Normal Apocalypse

Wired Science - Wed, 10/11/2017 - 07:00
A changing climate means fires, winds, and floods will devastate the places where humans meet the wild.
Categories: Bio

Retracting Bad Science Doesn’t Make It Disappear

Wired Science - Tue, 10/10/2017 - 10:00
Opinion: When a scientific paper is retracted, it can produce long-term aftershocks.
Categories: Bio