Misc. – Page 91 – Jonathan Eisen's Lab

Skeptical of this: Invitation to Participate in the East African Universities’ Lecture Series and a Safari

~~Hmm … this smells off. Must be as SCAM somewhere in here.~~
Updated 12/13/13. I do not think this is a SCAM. But I am not quite sure what it is.

———- Forwarded message ———-
From: Tours of Purpose (TOP) <info@toursofpurpose.com>
Date: Wed, May 23, 2012 at 9:29 PM
Subject: Invitation to Participate in the East African Universities’
Lecture Series and a Safari

Dear University of California Faculty and Staff:

Tours of Purpose, TOP, a professor exchange agency dedicated to the
development and improvement of economic, academic and general welfare
in East Africa (i.e., Uganda, Kenya, Tanzania, Rwanda and Burundi) is
hereby extending a humble invitation to you to participate in our
ongoing program of lecture series taking place in our local
universities, colleges, high schools, primary schools and other
academic institutions. Additionally, TOP would like to avail to you a
one in a lifetime opportunity to take a safari where you will see and
photograph lions, elephants, giraffes, leopards, zebras, hippos,
rhinos, among an array of wildlife, in addition to a rare opportunity
to visit the mountain gorillas and man’s closest relative, the chimp,
at a TOP’ scholars’ give away price. Winston Churchill took this trip
and immortally dabbed Uganda “The Pearl of Africa”, and Queen
Elizabeth was on such a safari when she learned that she had become
queen of England. The average visit lasts for about two weeks–with a
couple of days or so dedicated to visiting the said incredible African
wildlife reserves–although you may wish for your particular visit to
be shorter or longer. TOP would like to partner with a specific
professor, or any academician, in pursuing a possibility of coming to
East Africa to deliver lectures in any given dispositive academic
discipline. TOP will cooperate with you in arranging and customizing
your travel details to Africa, including picking you up at the airport
in TOP state of the art SUVs, booking fair accommodation, arranging
your meals, setting and managing your speaking schedule, taking you on
a safari trip and other tours, and ultimately delivering you to the
airport for your flight home. TOP invariably offers the option of one
being paired with another educator from North America or Europe during
this trip, although traveling alone in East Africa is not complicated
nor precarious at all.

Thus, if TOP secures your willingness to participate, TOP will, first,
discuss with you the financial side of it, including revealing what
assistance may be available for you in this regard so that you can
achieve your $1,200 or so round trip air ticket. Second, where a
Holiday Inn-style room costs about $180 a night in East Africa, TOP
offers you even better accommodation in our partnering hotel, Giraffe
Park Hotel, at $350 a week, breakfast and dinner inclusive. Lunch can
be packed or arranged very reasonably. As a TOP scholar, you also
qualify for $200 towards your travel expenses.

Consider, too, should you have plans of traveling to or through
Europe, why not shoot two birds with one stone by detouring through
East Africa for the instant, noble purpose and halve the costs, not to
mention the time to be saved or to be well used. Take note, too, that
in addition to some of your students who may either just want to
accompany you or do an internship here, you can invite your family and
friends as well.

As such, your willingness to participate dwarfs all financial
concerns, for TOP stands with you to make this trip not only
economical but, most importantly, simple to handle all around. In
fact, as an American educator, you are due to discover that your worth
to the vast world’s academic needs is patently inestimable and that
sharing your expertise inures a hidden fulfillment.

In sum, this email cannot answer all the questions you might have
regarding this trip, therefore, you are encourage to contact me so
that we can further this conversation, including chatting on the
phone, if you desire. Needless to say, I, or a TOP representative,
will be available to talk with you about either an immediate trip or
to muse about a distant future possibility for this lectureship, in
addition to whether TOP, in conjunction with our local institutions,
should promulgate a concrete, personalized proposal for your
consideration.

Lastly, feel very welcome to visit our website (http://www.toursofpurpose.com
) to learn more about us and to view photos and read up on
testimonials of past participants. Also, on the website you will be
able to either join us on Facebook or to follow us on twitter.

Therefore, we hope to hear from you soon.

Sincerely,

~Josephine Nakandi
Program Director

—
~~~~~~~~~~~~~~~~~~~~~~~~
Tours of Purpose, TOP
49 Nakawa Road, Suite 400
Kampala, Uganda, East Africa
Tel: +256 778 899 429
info@toursofpurpose.com
http://www.toursofpurpose.com
~~~~~~~~~~~~~~~~~~~~~~~~

UPDATE 12/12/13

Some miscellaneous stuff I found on the web relating to Tours of Purpose

Denis White, a Professor at U. Toledo has some doubts about financial behavior of “Teach and Tours Sojourner” which he reports has the same contact # as Tours of Purpose.
Teach and Tours Sojourners and Tours of Purpose both work with Stawa University

A reviewer of Teach and Tour Sojourners on Trip Advisor has some serious negative comments.

The “Meta Name” tag in the source of the current Tours of Purpose website reads:

” “

The “Title” tag in the current website reads “Tours of Purpose | Teach and Tour Sojourners, Kampala, Uganda, Entebbe”

Another negative review of TATS is here.

I note – there are also positive reviews out there of TATS and TOP. Hard to know just what is going on here. Could be that someone is trying hard and occasionally things go poorly. I have no idea.

Kimberly-Clark’s deceptive self serving PR regarding germs in the workplace #BadReportingToo

First I saw of this story was here: Study: Bacteria fills office break rooms – Local News – Houston, TX – msnbc.com

Something sounded off with this. I think it was the fact that it involved “Cleaning products company Kimberly-Clark” that raised some alarm bells. The involvement of Charles Gerba also left me a bit queasy as I have seen his name associated with a few recent “studies” which are basically germaphobia funded by cleaning product companies.

After looking around a bit I got discouraged at the whole thing and put it out of my head for a few hours. And then David Coil, a post doc in my lab, sent me a link to the press release behind this story. And boy is it a doozy.

The PR basically makes the following dubious statements or implications
* All bacteria are bad. The whole PR references a study that they imply is about detecting bacteria in various locations. And when they detect high levels they conclude this is bad. For example in the title “Where the Germs Are: New Study Finds Office Kitchens and Break Rooms are Crawling with Bacteria“. Or in the text: “If you thought the restroom was the epicenter of workplace germs you don’t want to know about office break rooms and kitchens” “office germ “hot-spots,”” “Office workers are potentially being exposed to illness-causing bacteria right in their own lunchrooms” and much more. Uggh. Not all bacteria are bad. Gerba and Kimberly-Clark must know this yet they purposefully mislead.

* Presence of ATP means presence of bacteria (and see above – this must imply presence of bad bacteria). Wow. Not sure what to say here. But they use a test for ATP which they say “ATP is present in all animal, vegetable, bacteria, yeast and mold cells. Detection of ATP indicates the presence of contamination by any of these sources. Everyday objects with an ATP reading of 300 or higher are considered to have a high risk for illness transmission.” No citation given. And sounds highly dubious to go from ATP – > risk for illness. Sounds completely dubious actually.

* That it is OK to make claims in Press Releases without presenting evidence behind the claims. The PR tries to make this all seem very scientific. Well, where is the paper behind this? They claim “The findings are from a study carried out by Kimberly-Clark Professional* and is believed to be one of the most detailed and comprehensive studies ever conducted on identifying workplace hotspots where germs can lurk.” Where is the actual data? Where are the methods described? Yuck.

Alas – despite the fact that the Press Release is at best a self serving piece of dubious scientific quality – the press has run with the story sucking up everything Gerba and Kimberly Clark are saying. Ugg. Here are some examples, many of which really do a poor job on the science and the conflicts of interest inherent in an unpublished study from a cleaning products company

I am getting sick and tired of crap like this. Kimberly-Clark may make some useful products. I don’t really know. But deceptive press releases like this suggest that their dedication to science is, well, low. They need to clean up their act.

Fall 2012 Introduction to Evolution (EVE 100) teaching position at #UCDavis

DEPARTMENT OF EVOLUTION AND ECOLOGY

FALL 2012

TEACHING POSITION AVAILABLE

LECTURER

Introduction to Evolution

(EVE 100)

FALL 2012 (September 24-December 14, 2012)

Responsibilities: A 60% position teaching EVE 100 – Introduction to Evolution (4 units). Lecture–3 hours, Discussion–1 hour. The course subject provides a general survey of the origins of biological diversity and evolutionary mechanisms. Estimated enrollment: 200

Requirements: Ph.D. and demonstrated effective teaching in the subject course or equivalent course.

Salary: Commensurate upon qualifications.

Please submit letter of application, including summary of qualifications, CV, two letters of recommendation and any applicable teaching evaluation summaries via the link below link which contains additional information about the position.

https://recruitments.ucdavis.edu/PositionDetails.aspx?PositionID=103&Title=Fall-2012-Lecturer—Introduction-to-Evolution-%28EVE-100%29

OPEN UNTIL FILLED. FOR FULL CONSIDERATION APPLICATION MUST BE RECEIVED BY JUNE 22, 2012.

This position may be covered by a collective bargaining unit.

The University of California is an Equal Opportunity/Affirmative Action Employer with a strong institutional commitment to the development of a climate that supports equality of opportunity and respect for diversity.

05/23/12

Something fishy with this story: bacteria in fish pedicures

Well, the title drew me in, without a doubt: Fish Pedicures: Bacteria in Your Foot Soak.

To start with _ i guess I have been out of touch as I have never heard of fish pedicures before. Sounds lovely I must say.

Though if you are considering doing this you might be dissuaded by some of the revelations in the article including that “fish are living creatures that deposit their waste products in the very water in which people are soaking” and “the impossibility of disinfecting or sanitizing live fish.”

Amazingly, fish pedicures are in fact apparently quite popular. So popular that there are multiple investigations relating to this practice including that “British authorities investigated a reported bacterial outbreak among 6,000 Garra rufa fish ” and “Last spring, British fish inspectors went to London’s Heathrow Airport and intercepted Indonesian shipments of the silver, inch-long freshwater carp destined for British “fish spas.”

And now – the reason for this article – there is a new report in the journal Emerging Infectious Diseases on “Zoonotic Disease Pathogens in Fish Used for Pedicure.” The article is actually somewhat fascinating and thanks to the CDC it is freely available.

Fun reading for the day …

Useful comparative analysis of sequence classification systems w/ a few questionable bits

There is a useful new publication just out: BMC Bioinformatics | Abstract | A comparative evaluation of sequence classification programs by Adam L Bazinet and Michael P Cummings. In the paper the authors attempt to do a systematic comparison of tools for classifying DNA sequences according to the taxonomy of the organism from which they come.

I have been interested in such activities since, well, since 1989 when I started working in Colleen Cavanaugh’s lab at Harvard sequencing rRNA genes to do classification. And I have known one of the authors, Michael Cummings for almost as long.

Their abstract does a decent job of summing up what they did

Background
A fundamental problem in modern genomics is to taxonomically or functionally classify DNA sequence fragments derived from environmental sampling (i.e., metagenomics). Several different methods have been proposed for doing this effectively and efficiently, and many have been implemented in software. In addition to varying their basic algorithmic approach to classification, some methods screen sequence reads for ’barcoding genes’ like 16S rRNA, or various types of protein-coding genes. Due to the sheer number and complexity of methods, it can be difficult for a researcher to choose one that is well-suited for a particular analysis.

Results
We divided the very large number of programs that have been released in recent years for solving the sequence classification problem into three main categories based on the general algorithm they use to compare a query sequence against a database of sequences. We also evaluated the performance of the leading programs in each category on data sets whose taxonomic and functional composition is known.

Conclusions
We found significant variability in classification accuracy, precision, and resource consumption of sequence classification programs when used to analyze various metagenomics data sets. However, we observe some general trends and patterns that will be useful to researchers who use sequence classification programs.

The three main categories of methods they identified are

Programs that primarily utilize sequence similarity search
Programs that primarily utilize sequence composition models (like CompostBin from my lab)
Programs that primarily utilize phylogenetic methods (like AMPHORA & STAP from my lab)

The paper has some detailed discussion and comparison of some of the methods in each category. They even made a tree of the methods

Figure 1. Program clustering. A neighbor-joining tree
that clusters the classification programs based on their similar attributes. From here.

In some ways – I love this figure. Since, well, I love trees. But in other ways I really really really do not like it. I don’t like it because they use an explicitly phylogenetic method (neighbor joining, which is designed to infer phylogenetic trees and not to simply cluster entities by their similarity) to cluster entities that do not have a phylogenetic history. Why use neighbor-joining here? What is the basis for using this method to cluster methods? It is cute, sure. But I don’t get it. What do deep branches represent in this case? It drives me a bit crazy when people throw a method designed to represent branching history at a situation where clustering by similarity is needed. Similarly it drives me crazy when similarity based clustering methods are used when history is needed.

Not to take away from the paper too much since this is definitely worth a read for those working on methods to classify sequences as well as for those using such methods. They even go so far as to test various web served (e.g., MGRAST) and discuss time to get results. They also test the methods for their precision and sensitivity. Very useful bits of information here.

So – overall I like the paper. But one other thing in here sits in my craw in the wrong way. The discussion of “marker genes.” Below is some of the introductory text on the topic. I have labelled some bits I do not like too much:

It is important to note that some supervised learning methods will only classify sequences that contain “marker genes”. Marker genes are ideally present in all organisms, and have a relatively high mutation rate that produces significant variation between species. The use of marker genes to classify organisms is commonly known as DNA barcoding. The 16S rRNA gene has been used to greatest effect for this purpose in the microbial world (green genes [6], RDP [7]). For animals, the mitochondrial COI gene is popular [8], and for plants the chloroplast genes rbcL and matK have been used [9]. Other strategies have been proposed, such as the use of protein-coding genes that are universal, occur only once per genome (as opposed to 16S rRNA genes that can vary in copy number), and are rarely horizontally transferred [10]. Marker gene databases and their constitutive multiple alignments and phylogenies are usually carefully curated, so taxonomic and functional assignments based on marker genes are likely to show gains in both accuracy and speed over methods that analyze input sequences less discriminately. However, if the sequencing was not specially targeted [11], reads that contain marker genes may only account for a small percentage of a metagenomic sample.

I think I will just leave these highlighted sections uncommented upon and leave it to people to imagine what I don’t like about them .. for now.

Anyway – again – the paper is worth checking out. And if you want to know more about methods used for classifying sequences see this Mendeley collection which focuses on metagenomic analysis but has many additional paper on top of the ones discussed in this paper.

Interesting new paper: "Proving universal common ancestry with similar sequences"

Just discovered an interesting paper by Leonardo de Oliveira Martins and David Posada. It is titled “Proving universal common ancestry with similar sequences.” It relates to a paper by Douglas Theobald: “A formal test of the theory of universal common ancestry. Nature 2010; 465:219-22.” Although the latter paper is not openly available the more recent one is.

The new paper is worth a look. Not sure about the Theobald one as I do not have access from home.

Am hoping Leonardo writes more about this in his blog: Bayesian Procedures in Biology ….

Mini post: Microbial forensics

A few months old here but there is a very interesting post from the Science Media Centre in New Zealand: Science Media Centre: Microbes in soil could help fight crime. The post describes attempts to use microbes in soil as part of forensic activities. This relates in many ways to my call for a “Field Guide to Microbes”.

I have been interested in microbial forensics for many years since I worked at TIGR on part of the project to study anthrax genomes. For those interested in microbe-related forensic activities I have created a Mendeley collection of references on the topic.

http://www.mendeley.com/groups/1147121/_/widget/29/5/

Microbial Forensics is a group in Biological Sciences, Law on Mendeley.

‘Danger and Evolution in the Twilight Zone’: Guest post by Randen Patterson and Gaurav Bhardwaj

Figure 1. PHYRN concept and work flow.

‘Danger and Evolution in the twilight zone’

I have been communicating with Randen Patterson on and off over the last five years or so about his efforts to try and study the evolution of gene families when the sequence similarity in the gene family is so low that making multiple sequence alignments are very difficult. Recently, Randen moved to UC Davis so I have been talking / emailing with jim more and more about this issue. Of note, Randen has a new paper in PLoS One about this topic: Bhardwaj G, Ko KD, Hong Y, Zhang Z, Ho NL, et al. (2012) PHYRN: A Robust Method for Phylogenetic Analysis of Highly Divergent Sequences. PLoS ONE 7(4): e34261. doi:10.1371/journal.pone.0034261.

Figure 8. Model for the Evolution of the DANGER Superfamily.

I invited Randen and the first author Gaurav Bhardwaj to do a guest post here providing some of the story behind their paper for my ongoing series on this topic. I note – if you have published an open access paper on some topic related to this blog I would love to have a guest post from you too. I note – I personally love the fact that they used the “DANGER” family as an example to test their method.

Here is their guest post:

A fundamental problem to phylogenetic inference in the “twilight zone” (<25% pairwise identity), let alone the “midnight zone” (<12% pairwise identity), is the inability to accurately assign evolutionary relationships at these levels of divergence with statistical confidence. This lack of resolution arises from difficulties in separating the phylogenetic signal from the random noise at these levels of divergence. This obviously and ultimately stymies all attempts to truly resolve the Tree of Life. Since most attempts at phylogenetic inferences in twilight/midnight zone have relied on MSA, and with no clear answer on the best phylogenetic methods to resolve protein families in twilight/midnight zone, we have presented rest of this blog post as two questions representative of these problems.

Question1: Is MSA required for accurate phylogenetic inference?

Our Opinion: MSA is an excellent tool for the inference from conserved data sets, but it has been shown by others and us, that the quality of MSA degrades rapidly in the twilight zone. Further, the quest for an optimal MSA becomes increasingly difficult with increased number of taxa under study. Although, quality of MSA methods has improved in last two decades, we have not made significant improvements towards overcoming these problems. Multiple groups have also designed alignment-free methods (see Hohl and Ragan, Syst. Biol. 2007), but so far none of these methods has been able to provide better phylogenetic accuracy than MSA+ML methods. We recently published a manuscript in PLoS One entitled “PHYRN: A Robust Method for Phylogenetic Analysis of Highly Divergent Sequences” introducing a hybrid profile-based method. Our approach focuses on measuring phylogenetic signal from homologous biological patterns (functional domains, structural folds, etc), and their subsequent amplification and encoding as phylogenetic profile. Further, we adopt a distance estimation algorithm that is alignment-free, and thus bypasses the need for an optimal MSA. Our benchmarking studies with synthetic (from ROSE and Seqgen) and biological datasets show that PHYRN outperforms other traditional methods (distance, parsimony and Maximum Liklihood), and provides significantly accurate phylogenies even in data sets exhibiting ~8% average pairwise identity. While this still needs to be evaluated in other simulations (varying tree shapes, rates, models), we are convinced that these types of methods do work and deserve further exploration.

Question 2: How can we as a field critically and fairly evaluate phylogenetic methods?

Our Opinion: A similar problem plagued the field of structural biology whereby there were multiple methods for structural predictions, but no clear way of standardizing or evaluating their performance. An additional problem that applies to phylogenetic inference is that, unlike crystal structures of proteins, phylogenies do not have a corresponding “answer” that can be obtained. Synthetic data sets have tried to answer this question to a certain extent by simulating protein evolution and providing true evolutionary histories that can be used for benchmarking. However, these simulations cannot truly replicate biological evolution (e.g. indel distribution, translocations, biologically relevant birth-death models, etc). In our opinion, we need a CASP-like model (solution adopted by our friends in computational structural biology), where same data sets (with true evolutionary history known only to organizers) are inferred by all the research groups, and then submitted for a critical evaluation to the organizers. To convert this thought to reality, we hereby announce CAPE (Critical Assessment of Protein Evolution) for Summer 20132. We are still in pre-production stages, and we welcome any suggestions, comments and inputs about data sets, scoring and evaluating methods.

Bhardwaj, G., Ko, K., Hong, Y., Zhang, Z., Ho, N., Chintapalli, S., Kline, L., Gotlin, M., Hartranft, D., Patterson, M., Dave, F., Smith, E., Holmes, E., Patterson, R., & van Rossum, D. (2012). PHYRN: A Robust Method for Phylogenetic Analysis of Highly Divergent Sequences PLoS ONE, 7 (4) DOI: 10.1371/journal.pone.0034261

Quick post – new paper of interest on "The Infinitely Many Genes Model …"

This paper seems of potential interest: The Infinitely Many Genes Model for the Distributed Genome of Bacteria by Franz Baumdicker, Wolfgang R. Hess, and Peter Pfaffelhuber

Abstract:

The distributed genome hypothesis states that the gene pool of a bacterial taxon is much more complex than that found in a single individual genome. However, the possible fitness advantage, why such genomic diversity is maintained, whether this variation is largely adaptive or neutral, and why these distinct individuals can coexist, remains poorly understood. Here, we present the infinitely many genes (IMG) model, which is a quantitative, evolutionary model for the distributed genome. It is based on a genealogy of individual genomes and the possibility of gene gain (from an unbounded reservoir of novel genes, e.g., by horizontal gene transfer from distant taxa) and gene loss, for example, by pseudogenization and deletion of genes, during reproduction. By implementing these mechanisms, the IMG model differs from existing concepts for the distributed genome, which cannot differentiate between neutral evolution and adaptation as drivers of the observed genomic diversity. Using the IMG model, we tested whether the distributed genome of 22 full genomes of picocyanobacteria (Prochlorococcus and Synechococcus) shows signs of adaptation or neutrality. We calculated the effective population size of Prochlorococcus at 1.01 × 1011 and predicted 18 distinct clades for this population, only six of which have been isolated and cultured thus far. We predicted that the Prochlorococcus pangenome contains 57,792 genes and found that the evolution of the distributed genome of Prochlorococcus was possibly neutral, whereas that of Synechococcus and the combined sample shows a clear deviation from neutrality.

Wish they had gone beyond these two cyanobacteria … but still seems of possible interest. Baumdicker, F., Hess, W., & Pfaffelhuber, P. (2012). The Infinitely Many Genes Model for the Distributed Genome of Bacteria Genome Biology and Evolution, 4 (4), 443-456 DOI: 10.1093/gbe/evs016

iEvoBio Call for Challenge entries for conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio)

From: Hilmar Lapp
Date: Thu, May 10, 2012 at 11:27 AM
Subject: [iEvoBio] Call for Challenge entries for conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio)
To: iEvoBio Announcements

Many trees enter.
Fresh analysis ensues.
New insights emerge.

As a reminder, the iEvoBio conference is again holding a Challenge competition in 2012, this time on the theme, "Synthesizing Phylogenies." Further information on the nature of challenge entries and how to submit them can be found on the iEvoBio website at http://ievobio.org/challenge.html. Submissions are due by June 25, 2012. Cash prizes will be awarded for first place (USD 1,500) and runner-up entries. The winning entries will be selected by a vote of the iEvoBio meeting participants.

Also, alongside the iEvoBio Challenge, 2012 iEvoBio sponsor Biomatters Ltd is running the Geneious Challenge. The goal of this challenge is to develop a new plugin to Geneious Pro, using the public API, that enables a new and exciting visualization or analysis. The winning entry will receive a $1000 cash prize, and all entrants who submit by the deadline will receive a 12-month subscription license. The deadline for the Geneious Challenge is the same as for the iEvoBio Challenge. See http://ievobio.org/geneious_challenge.html for more information.

More details about the iEvoBio conference and program are available at http://ievobio.org. You can also find continuous updates on the conference’s Twitter feed at http://twitter.com/iEvoBio and Google+ page, or subscribe to the low-traffic iEvoBio announcements mailing list at http://groups.google.com/group/ievobio-announce.

iEvoBio 2012 is sponsored by the US National Evolutionary Synthesis Center (NESCent) and by Biomatters Ltd., in partnership with the Society for the Study of Evolution (SSE) and the Systematic Biologists (SSB).

The iEvoBio 2012 Organizing Committee:
Hilmar Lapp, US National Evolutionary Synthesis Center (chair)
Robert Beiko, Dalhousie University
Nico Cellinese, University of Florida
Robert Guralnick, University of Colorado at Boulder
Rebecca Kao, Denver Botanic Gardens
Ellinor Michel, Natural History Museum, London
Nadia Talent, Royal Ontario Museum
Andrea Thomer, University of Illinois at Urbana-Champaign

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