…which led to the (in)famous Scopes Trial. On May 5, 1925 John Scopes was charged and subsequently tried, found guilty, and fined $100 for teaching Evolution, a violation of Tennessee’s Butler Act. The trial became a battleground for science vs. religion, evolution vs. creationism, and the interpretation of the Establishment Clause and Freedom of Speech in the US constitution.

I published a blog post two years ago, on the 85th anniversary of the trial, July 2010. Today  marks the 87th anniversary of the arrest, so it seems like a good occasion to repost. Especially since there is still some work needed in the area of teaching evolution:

Source Wikimedia Commons. Credit: John D. Croft. Based on: New Scientist Magazine 2006 191:2565 p11

To follow is the original post: “The Scope(s) of Substance”,  from July 29, 2010. Still relevant, I believe:

Bora Zivkovic, the BUCA (Best Universal Common Ancestor) of science bloggers has tagged this blog with with a Blog of Substance award. As a grateful recipient of this award I am obligated to do two things:
1. Sum up my blogging motivation, philosophy and experience in exactly 10 words.
2. Pass this award on to 10 other blogs.

Of course, I never do anything without researching it first, because I am such an awesome scientist, or detail-oriented !@#*^, depending on whether you ask me or my students. So I looked up “substance” in the Merriam-Webster dictionary. Here is what I found:

Main Entry: sub·stance
Pronunciation: \ˈsəb-stən(t)s\
Function: noun
Etymology: Middle English, from Anglo-French, from Latin substantia, from substant-, substans, present participle of substare to stand under, from sub- + stare to stand — more at stand
Date: 14th century

1 a : essential nature : essence b : a fundamental or characteristic part or quality c Christian Science : god 1b
2 a : ultimate reality that underlies all outward manifestations and change b : practical importance : meaning, usefulness
3 a : physical material from which something is made or which has discrete existence b : matter of particular or definite chemical constitution c : something (as drugs or alcoholic beverages) deemed harmful and usually subject to legal restriction

4 : material possessions : property

Hmmm… 2a and 2b seem to be relevant. Perhaps 3c should be too, as my blogging could be construed harmful to other more productive activities, which I am obviously not engaged with at this moment. Actually you, gentle reader, are not engaged in more productive activities either right now. Be that as it may, the word substance does seem to have an air of permanence about it, which is contrary to the perceived ephemeral nature of blogging. Bora is actually one of the people who are doing something about making blogs less ephemeral by publishing The Open Laboratory collection (full disclosure: I’m published in the 2009 book) and by supporting science bloggers, blogging and activities wherever they may be. This makes me so happy to be among Bora’s chosen 10 (OK, 11, he cheated a bit) among the hundreds of blogs he must be reading. Thanks Bora!

I do wonder though, eighty-five years from now, how many of us science bloggers would be remembered for our blogging? Well, maybe not as individuals, but what kind of impact are we having now, and how much will it remain 85 years from now? Hopefully as a collective, science bloggers are impacting the understanding of science, which is one of the reasons I am blogging. Hopefully, we do have substance, as a group if not as individuals.

Why eighty-five years? Well, the answer to that brings me to the main topic (substance?) part of this post, which is the anniversary of the Scopes trial. This month, 85 years ago, a schoolteacher in Tennessee was convicted of a high misdemeanor for violating the State of Tennessee’s Butler Act which prohibited the teaching of evolution in any of the state’s public schools and universities. He was fined $100.

PUBLIC ACTS

OF THE

STATE OF TENNESSEE

PASSED BY THE

SIXTY – FOURTH GENERAL ASSEMBLY

1925

________

CHAPTER NO. 27

House Bill No. 185

(By Mr. Butler)

AN ACT prohibiting the teaching of the Evolution Theory in all the Universities, Normals and all other public schools of Tennessee, which are supported in whole or in part by the public school funds of the State, and to provide penalties for the violations thereof.

Section 1. Be it enacted by the General Assembly of the State of Tennessee, That it shall be unlawful for any teacher in any of the Universities, Normals and all other public schools of the State which are supported in whole or in part by the public school funds of the State, to teach any theory that denies the story of the Divine Creation of man as taught in the Bible, and to teach instead that man has descended from a lower order of animals.

Section 2. Be it further enacted, That any teacher found guilty of the violation of this Act, Shall be guilty of a misdemeanor and upon conviction, shall be fined not less than One Hundred $ (100.00) Dollars nor more than Five Hundred ($ 500.00) Dollars for each offense.

Section 3. Be it further enacted, That this Act take effect from and after its passage, the public welfare requiring it.

Passed March 13, 1925

W. F. Barry,

Speaker of the House of Representatives

L. D. Hill,

Speaker of the Senate

Approved March 21, 1925.

Austin Peay,

Governor.

Seems incredible at this day an age… or maybe not so incredible given recent events in Louisiana.

William Jennings Bryan, counsel for the prosecution, attacking evolution

The city of Dayton as the organ grinder profiting from the Scopes trial

The trial, which originated as something of a publicity affair for the town of Dayton, Tennessee, quickly became a battleground for evolution vs. creation. In the short term, the trial actually increased the number of anti-evolution bills proposed in different state legislatures in the US. In the long term, however, Tennessee vs. Scopes is seen as a watershed moment in the teaching and public acceptance of evolution, and has had long terms ramifications in the US and internationally. Scopes himself spoke only once at the trial, was not called to testify, and only had this to say when granted a statement after sentence was passed:

Your honor, I feel that I have been convicted of violating an unjust statute. I will continue in the future, as I have in the past, to oppose this law in any way I can. Any other action would be in violation of my ideal of academic freedom — that is, to teach the truth as guaranteed in our constitution, of personal and religious freedom. I think the fine is unjust.

Now that is substance.

Back to the award; I still have some conditions to fulfill:

1. Sum up your blogging motivation, philosophy and experience in exactly 10 words.

¹Blogging ²motivation, ³philosophy ⁴and ⁵experience ⁶cannot ⁷be ⁸summed ⁹in ¹⁰ten ¹¹words.

2. Pass this award on to 10 other blogs

Given the 10ⁿ growth rate of tagged blogs, chain-letter fashion, I wonder about how this Blogging with Substance award has originated. Search engines was no help, as so many blogs are now tagged with the Blogging with Substance. If someone has an answer, let me know. Anyhow, here are my 10 tags, based on what I am reading nowadays, ephemerality of blogging substance, and all that jazz. Tough choices though, so many good blogs out there:

1. Blue Collar Bioinformatics

2. Sandwalk

3. Thoughtomics

4. The Loom

5. Mike the Mad Biologist

6. Genomics, Evolution and Pseudoscience

7. Circle of Complexity

8. Buried Treasure

9. The Tree of Life

10. Mystery Rays form Outer Space

Final word: if this post seems a bit confused, and you are not sure that you are “getting it”, well, that’s this post’s substance.

Dear Dr.Iddo Friedberg,    

Greeting from OMICS Group!

I came across your contribution entitled “Biopython: freely available Python tools for computational molecular biology and bioinformatics” published in the Journal of Bioinformatics and thought your expertise would be an excellent fit for Toxicology-2012 Conference that OMICS Group is hosting.

 

I’m just wondering how many legitimate calls for participation I am missing due to the increasing amounts of conference spam in my inbox.

Great meeting:  Biocuration 2012, Georgetown University, DC.  When I leave a meeting with my head exploding with new ideas and a need to try them all out at once, I know I got my money’s worth, and then some. Even a three hour flight delay followed by discovering my car with a dead battery at 1am at the deserted Dayton Airport parking lot did not dampen my enthusiasm upon return. I will make sure my dome light is off before I leave my car  the next time though. To follow are bits and pieces from the meeting I enjoyed. I’m doing this mostly from memory, two days later, so I may have an addendum once I get my notes together.

What is biocuration? Well, anything that has to do with annotating, labeling, indexing, identifying biological entities. Almost exclusively genes in this conference. Genome databases, especially those of model organisms, employ curators to annotate, check and re-annotate the genomic data Here’s a more elaborate explanation, taken from the website of the International Society for Biocuration:

Biocuration involves the translation and integration of information relevant to biology into a database or resource that enables integration of the scientific literature as well as large data sets. Accurate and comprehensive representation of biological knowledge, as well as easy access to this data for working scientists and a basis for computational analysis, are primary goals of biocuration.

The goals of biocuration are achieved thanks to the convergent endeavors of biocurators, software developers and researchers in bioinformatics. Biocurators provide essential resources to the biological community such that databases have become an integral part of the tools researchers use on a daily basis for their work.

Day 1 started off with many community annotation tools. I thought that the Wikipedia model for annotation was dead, but maybe I’m wrong. Many community efforts use a large number of experts, as opposed to a huge number of non-experts, which is what the speakers at the first session were discussing. Pombase (whose title drew some chuckles from the French speakers at my table), the Tetrahymna Genome Database Wiki and the Gene Wiki were presented. The Gene Wiki, presented by Andrew Su from TSRI is a bona-fide crowdsourcing approach, not just Wikipedia-like but actually comprised of a set of 10,000 gene definition stubs folded into Wikipedia. Jennifer Harrow from Sanger presented a poster with an accession model of annotations: the “blessed annotator” who has been trained for 3 months and has the run of the wiki, and the “gatekeeper”, who has been trained in a 2-day workshop, and whose contributions need to be monitored. Lots of talks about trusted annotators, etc. Perhaps we should look to cryptography’s “circles of trust” to enable trusted annotations yet increase the number of curators. (I use “curation” and “annotation” interchangeably throughout.)

An afternoon workshop, discussed who are biocurators. If you are a biocurator, there’s a good probability you are 31-50 years young (80%), female (60%), with a PhD (76%), been through the academic mill and found it to be a bad fit for one reason or the other. You like your work, you rarely burn out, it is challenging and stimulating, you are not in it for the money. (Few people in non-industry science are.)  Actually, since non-profit science is run on soft money, funding is a serious concern, and your job may have a shorter half-life that you would care for it to have, as you are probably employed on a 3-5 year contract. Your boss is rarely a biocurator her/himself, which may mean that your job description may sometimes be ill-defined.

After  that, there was a  whole session devoted to curation workflows and tools. If  you are setting up your own genomic database, check these out: WebApollo,  CvManGO and the Reactome. Attila Csordas from EBI presented PRIDE, a tool for curating proteomic data. While proteomic data are growing, there are few choices of software tools to annotate them. So PRIDE is a welcome player in the field.

 Day 2 had a “Genomics, metagenomics comparative genomics” session, only without the metagenomics.  What I really liked was the ViralZone resource for viral genomes, out of SIB. High time someone did this for the most abundant biological particle on Earth, and the one responsible for most diversity in life.

The breakout sessions were my favorite, getting a change to interact with like-minded people interested in similar questions. (That is, those that share my prejudices.) I went to the one organized by Marc Robinson-Rechavi and Frederic Bastian which dealt with the question of quality in gene annotation.  Here is the problem: when we annotate a gene with a function (or functions), we also need to say what is the evidence that brought us to think that this gene does what it does. The most popular vocabulary for annotating genes is the Gene Ontology or GO. GO provides us with evidence codes which allow the curator to say what is the evidence for the function they assign to a gene. Those range from experimental evidence codes such as “inferred from mutant phenotype” which are always entered by a human curator, to “Inferred from Electronic Annotation” which have no human oversight. These evidence codes are used as a proxy for quality: people generally tend to accept that evidence from an experiment may be stronger evidence that that gene does what it does than an electronic one. That may not necessarily be true. For example, high-throughput experiments that results in many genes getting assigned with annotations wholesale. Even with the uncharacteristically low) 5% error rate, a single paper used as a source from which 5,000 genes are annotated would result in 25 wrongly annotated genes.  In addition, these types of experiments supply annotations that are not very specific, such as “protein binding” or “embryonic development”, terms that in many cases are too general to be useful. On  the other hand, Nives Škunca of ETH Zurich has shown a beautiful study about how fully automated annotations may not be as inferior to human-curated ones as most people think, with some caveats. (Note: Nives also showed her work in a poster that won the best poster award at the meeting, and this work has just been accepted to PLoS Computational Biology. I will try to blog more about it once it’s published, it’s really brilliant.) The discussion revolved around how we should ascertain the quality of annotations, what would be considered a useful annotation, and how can we establish trustworthiness. Seems like there is quite a bit of work to be done, as people are only beginning to realize that this is a more complex problem than we thought. A major player in this will be the Evidence Ontology or ECO, an elaborate ontology in the making describing lines of evidence for gene annotation.

Day 3: Atilla Csordas, whom I mentioned earlier, organized an unconference session early morning. A few of us gave brief talks there. Ben Good from Andrew Su’s lab talked about biocuration through games, with harnessing  The idea is to do for biocuration what fold.it has done for protein folding. The Dizeez game quizzes you about diseases related to genes, and scores you according to how well you link genes to diseases. But as Andrew says on his blog:

 Generally, the gene-disease links in structured databases will be reasonably correct (though likely not at all complete). When we analyze the game logs in aggregate, we expect that players’ answers will generally reinforce what’s already known. But given enough game player data, also expect that we’ll see multiple instances of gene-disease links that aren’t reflected in current annotation databases. And these are candidate novel annotations.

So there may be something there, although it is not the “wisdom of the crowds” that is being exploited, since I imagine that only people with advanced degrees in their field can contribute to Dizeez. You can see games from the Su lab on genegames.org. Sean Mooney from Buck talked about the Statistical Tracking of Ontological Phrases (STOP) project. The idea here is to automatically enrich GO annotation of genes with other ontologies, to get a more comprehensive description of their function, especially when it comes to disease.  I talked about the Critical Assessment of Function Annotations (we finally submitted the paper, yay!).  Atilla talked about annotating proteomic data.

Great meeting. A big thank you to the organizers, it went without a hitch.  Logistics, food, coffee were all fantastic. Looking forward to Cambridge nest year! EDIT: a virtual special issue of Database has been published for this meeting, Some of the talks are there as papers. Open Access, of course.

Finally, my favorite promotional item from the meeting:

I guess that as a CAFA organizer, I should really contribute to the second page. And I will. But I really don’t mind if someone else jump-starts it.

http://en.wikipedia.org/wiki/Protein_function_prediction

http://en.wikipedia.org/wiki/Critical_Assessment_of_Function_Annotation

It is with no inconsiderable degree of reluctance that I decline the offer of any Paper from you. I think, however, you will upon reconsideration of the subject be of opinion that I have no other alternative. The subjects you propose for a series of Mathematical and Metaphysical Essays are so very profound, that there is perhaps not a single subscriber to our Journal who could follow them.

David Brewster, physicist and mathematician and inventor acting as editor of The Edinburgh Journal of Science to Charles Babbage, mathematician, philosopher, inventor and mechanical engineer; father of the computer circa 1821.

Hats off to Jonathan Eisen for hosting this activity on his blog. (I’ll keep mine on, thank you. It’s raining cats and dogs here right now).

A couple of weeks ago I posted a discussion about two papers that challenged the ortholog conjecture. Briefly, both papers stated that orthologs may not be such great predictors for molecular function. One study from  Indiana University by  has shown that paralogs may be better predictors than orthologs for molecular function. Or, at the very least, paralogs should not be excluded as predictors. This paper has generated quite a bit of interest and controversy. Consequently, Eisen has invited Matthew Hahn, the lead author to write about “the story behind the story” in Eisen’s well-read blog. The post is a great read, and has generated an animated discussion in the comments area. You do need to clear quite a bit of time to go through both Hahn’s guest post and the comment thread: the topic is a rather complex one, and as explained in the comments thread, one problem is that the ‘ortholog conjecture’ itself seems to be not well-defined.

I kept checking in to Eisen’s blog to read the elongating comment thread. It seems that now a special session on the topic may be in the works for the 2012 annual meeting of the Society for Molecular Biology and Evolution following this discussion. So great to see such an involved community getting together.

1. This is crap. (Rare).

2. This is terrific. (Even rarer).

3. This can be OK, but they really need to fix A, B & C. (fairly common).

4. If I only knew what they meant in point A, I could say whether they need to fix A, B & C or just B & C, or maybe explaining A will clarify to me that B need not be fixed at all.(Really common!)

The things is, sometimes draft manuscript are good, but unclear on a very specific and crucial point. Like point A.  The lack of clarity is not necessarily due only to bad writing. Sometimes it is very hard to describe a new idea or method. After all, it is new, right? So no-one has described it before and finding the correct way to describe you new idea or method can be very tricky. Some people use analogies (like me, I love analogies). But an analogy can be over interpreted, and then mis-interpreted, and your intricately concocted explanation is all shot. Then again, some authors do not use analogies, but explain their methods very formally. A reader who is very visual (like myself) would like to see a some graphic depiction of the method, but that may not be possible, or the author’s graphic rendering skills are not good enough.  In any case, I seem to get a lot into the position where my opinion of the paper hinges around one or two crucial details. If this were a seminar, and the author was talking about her work, I would just ask her to clarify the point. But I cannot do that when reviewing an article. Which leaves me with asking to perform major revisions, which sets the paper into a serious delay mode or sometimes reject because other reviewers have been less amenable.   (As an aside, I have noticed some reviewers  just let  the ambiguity of point A slide. This usually happens if the last author is Dr. Bigschotte, holder of the Endowed Golden Chair professorship of Biowizardry).

But maybe I can ask that clarification question of the author, or even have a brief dialogue? Anonymous email/chat technology can do wonders for shortening the turnover time of papers and clarifying issues. I am not saying that writers are now given a free license to write badly. But if needed, a chat session or email exchange monitored by the editor could really help push a paper through (or away). The exchange should be very brief, topical, logged (with the referee anonymized). The session should be requested by the referee, with very specific questions. The number of back-and-forth exchanges should be limited.

As a referee, I see myself more as a midwife (or whatever is the male counterpart) than a gatekeeper. I am not interested so much in keeping bad papers out (that is actually fairly easy), but letting good science in, even when it presents itself feet first and covered in gunk (OK, that was a rotten analogy, but you know what I mean). Anything that can ease this process is more than welcome.

So… any takers? Or is this a terrible idea? Better yet, has something like this been done?

PS: actually, as an author, I sometimes receive reviewer comments which I do not quite understand. This is even worse, since if I don’t address the issue in the way the reviewer asked for, it can spell the death of my paper. So this mechanism of quick dialogue between reviewer and author can work well both ways.

I am learning a lot about scavenging tweets.  Apparently, I cannot go back beyond a few days using the api.search() function. Hence, if I try to search for all the #AFPCAFA11 hashtags I will get nothing from the meeting’s dates. But if I look for a user’s tweets using api.user_timeline() I can go back for months on the users timeline, and then filter out the tweets with the relevant hashtags.  Since it seems I was the principal twiterrer in that meeting, I’m putting up my tweets here. Apologies to the others who recorded the meeting using Twitter: if you want your tweets included, drop me a line with your Twitter user name.

Thu Jul 14 16:04:22 2011 At Vienna. #ISMB #AFPCAFA11 #ISMB11
Thu Jul 14 16:07:34 2011 At Vienna #ISMB #AFPCAFA11 Curious who is the best protein function predictor? Join us. http://bit.ly/htv3J7
Fri Jul 15 09:10:24 2011 Jesse Gillis from UBC on a function prediciton post-mortem #AFPCAFA11 #ISMB
Fri Jul 15 09:12:11 2011 This is going to be fun. Jesse Gillis UBC. Postmortem on MouseFunc #ISMB #AFPCAFA11 Precision / Recall of 0.06… argh.
Fri Jul 15 09:14:14 2011 http://bit.ly/obSISi MouseFunc experiment #AFPCAFA11 #ISMB
Fri Jul 15 09:28:58 2011 Multifunctionality affect prediction profoundly. Take-home message from Jesse Gillis’ talk #AFPCAFA11 #ISMB
Fri Jul 15 09:31:22 2011 Next up: Meghana Chitale from @kiharalab #ISMB #AFPCAFA11
Fri Jul 15 09:36:44 2011 Co-occurrence association scores. CAS Lookiong for associations across GOs: between a BPO term and a CCO term, for example. #AFPCAFA11
Fri Jul 15 09:41:17 2011 Missing enzyme predictions. My fav. Chtiale at #ISMB #AFPCAFA11
Fri Jul 15 09:56:08 2011 Yanay Ofran from Bar ilan U about multifunctionality. How to assess the number of false positives? #ISMB #AFPCAFA11
Fri Jul 15 09:56:44 2011 Prediciton of photosynthesis in an elephant genome is a good sign of false positives. Yanay #ISMB #AFPCAFA11
Fri Jul 15 10:02:56 2011 Precision of short motifs is surprisingly high. Yanay, #ISMB #AFPCAFA11
Fri Jul 15 10:05:42 2011 short motifs identify functional motifs. Whereas homology identifies evolutionary relatedness. #AFPCAFA11 #ISMB
Fri Jul 15 10:09:14 2011 Next up: me. #AFPCAFA11 #ISMB
Fri Jul 15 11:44:45 2011 David Jones from UCL is talking about his #AFPCAFA11 predictions. Many different features. #ISMB
Fri Jul 15 11:47:18 2011 profile-profile fold recognition works well in Function prediction as well. #AFPCAFA11 #ISMB
Fri Jul 15 11:53:02 2011 Jones talking about why it is unhealthy to exercise in the morning. #AFPCAFA11 #ISMB generation of free radicals. #excusesaregreat
Fri Jul 15 11:56:43 2011 49,000 features in an SVM. #ISMB #AFPCAFA11
Fri Jul 15 11:57:47 2011 Hard to believe no redundancy in 49K features…. #ISMB #AFPCAFA11
Fri Jul 15 11:59:17 2011 “I like this plot and I would make a t-shirt out of it, but in terms of scientific value its worth is zero”. Jones, #AFPCAFA11 #ISMB
Fri Jul 15 12:01:09 2011 New term heard for a 2nd time at #ISMB #AFPCAFA11 “postdiction” as opposed to “prediction”. #notsurewhatitmeans
Fri Jul 15 12:16:49 2011 Lightning talks at #AFPCAFA11 #ISMB starting now
Fri Jul 15 12:35:51 2011 Mary Jo Ondrechen on SALSA at #AFPCAFA11 #ISMB structure –> function.
Fri Jul 15 12:36:45 2011 CDEHKRY make up 75% of all catalytic sites. Mary Jo #ISMB #AFPCAFA11
Fri Jul 15 12:50:50 2011 Jeffrey Yunes from UC Berkeley on SIFTER from Steven Brenner’s lab. #AFPCAFA11 #ISMB
Fri Jul 15 14:28:20 2011 Patrik Koskinen on a function prediction method called PANNZER. This will roll over well. #ISMB #AFPCAFA11
Fri Jul 15 14:30:30 2011 More information on PANNZER and the other methods at #AFPCAFA11 here: http://bit.ly/l9ayW9 #ISMB11
Fri Jul 15 14:33:16 2011 Koskinen mentioning Biothesaurus http://bit.ly/rnHdzp which removes errors due to synonyms #AFPCAFA11 #ISMB
Fri Jul 15 14:43:09 2011 Question: “How do you pronounce the name of that volcano that erupted in Iceland?” Answer: “I don’t”. Koskinen #AFPCAFA11 #ISMB
Fri Jul 15 14:50:27 2011 Olivier Lichtarge on using Evolutionary Trace Annotation (ETA) for function prediction. #AFPCAFA11 #ISMB
Fri Jul 15 14:51:12 2011 A network of protein structure networks. Memories of fragnostic. #AFPCAFA11 #ISMB
Fri Jul 15 14:52:49 2011 Using network diffusion to annotate protein structures. Lichtargee. #AFPCAFA11 #ISMB
Fri Jul 15 14:57:19 2011 compressing a clique to a star graph by adding a pseudo-node. Reduces problem from O(n^2) to O(n). Lichtarge #ISMB #AFPCAFA11
Fri Jul 15 15:09:17 2011 Amos Bairoch: of prosite, swissprot and expasy fame #AFPCAFA11 #ISMB
Fri Jul 15 15:12:51 2011 Due to alt-splicing and PTM 20,000 human genes –> 5M different molecules! Bairoch #AFPCAFA11 #ISMB
Fri Jul 15 15:15:50 2011 Status codes of human protein function annotations: Maybe, potentially, putative, expected and hopefullly. Bairoch #ISMB #AFPCAFA11
Fri Jul 15 15:17:10 2011 >100 GPCRs for which we do not know the ligand. Bairoch #ISMB #AFPCAFA11
Fri Jul 15 15:19:13 2011 Bairoch now talking about CALIPHO. 1)experimental verification of human protein function; 2)enable bioinformatics for same. #ISMB #AFPCAFA11
Fri Jul 15 15:20:44 2011 “How many ppl in this room have never used swissprot”. 0. #AFPCAFA11 #ISMB
Fri Jul 15 15:23:24 2011 Bairoch looks at small <100aa intracellular protiens in experimental assays. #AFPCAFA11 #ISMB
Fri Jul 15 15:26:26 2011 Interesting proteins are expressed in olfactory pits of zebrafish. I didn’t know fish smell. #AFPCAFA11 #ISMB
Fri Jul 15 15:33:09 2011 If you get a new function, you cannot predict it, because of no ontology (yet). #AFPCAFA11 #ISMB
Sat Jul 16 06:58:43 2011 Predrag Radivojac explaining the vagaries of GO annotated databases #AFPCAFA11 #ISMB
Sat Jul 16 06:59:48 2011 Assessment of protein function prediction methods going on now in Hall L #ISMB #AFPCAFA11
Sat Jul 16 07:04:08 2011 Radivojac: “It’s possible to achieve a precision of 1, it just won’t happen”. #AFPCAFA11 #ISMB
Sat Jul 16 07:29:50 2011 Assessment of protein function prediction methods going on now in Hall L #ISMB #AFPCAFA11 http://bit.ly/htv3J7 Sean Mooney is up.
Sat Jul 16 08:05:49 2011 Christine Orengo on her team’s work at #AFPCAFA11
Sat Jul 16 08:06:28 2011 Orengo says that they are not really function predictors, but evolutionary classifiers #AFPCAFA11 #ISMB
Sat Jul 16 09:18:03 2011 Shaneka Simmon from Jackson State on predicting functions associated with biofeuls – universal stress protein domains. #AFPCAFA11 #ISMB
Sat Jul 16 09:21:30 2011 Simmons: look for diversity of universal stress response genes. in Rhodopseudomonas palustris. #AFPCAFA11 #ISMB11
Sat Jul 16 11:33:52 2011 http://yfrog.com/kevdmbqj #AFPCAFA11 #ismb discussion panel now
Sat Jul 16 14:46:07 2011 Wyatt shows that paralogs actually give better annotation transfer than orthologs. http://bit.ly/nWShuB #AFPCAFA11 #ISMB
Sat Jul 16 14:47:17 2011 Wyatt’s claim runs contrary to common wisdom. Which is good http://bit.ly/nWShuB #AFPCAFA11 #ISMB
Thu Jul 21 22:42:34 2011 After all the talk about standards at #AFPCAFA11 #ISMB this is very timely: http://xkcd.com/927/

I have recently been invited to Google+, (thanks Ruchira!)  and as social timesucks go, it is quite enjoyable.  Here are my first impressions about g+. In a nutshell: g+’s attempt at compartmentalized communication is laudable, but falls short of the mark. Mainly because, no social network can emulate the real-life way we communicate (or not) with the people we know. Not that g+ ‘s goal  emulating real-life social interactions (for those of us who still have them), but let me explain myself.

Compartmentalized communication is what we do every day: my wife reminds me about my medical appointment, but not in front of the kids, because the little one still freaks out over doctors. At work I tell someone I need to cover for me teaching (because I need to take a day off) but not my other colleagues (none of their damn business). While waiting at the Doctor’s office I receive an email that my paper is finally published. I email the info to all the co-authors, and I may also just put it up on Facebook, because I am kinda proud. But of my 100 or so FB “friends” maybe 30 will understand why this is important to me.

The average Facebook user just likes to post stuff on his wall, assuming interested friends will be reading and posting back. Most FB friends are not real friends, in the social sense, but many are acquaintances, professional colleagues, and people you just do not want to turn away when you get a FB Friend Request.  G+ breaks those myriad people into circles: family, friends, acquaintances, followers. I also added “bioinformatics” and “science”.  This compartmentalization by circles initially makes sense because it is more in harmony with what our social life is supposedly like. We have our family, out really good friends, our drinking buddies, our professional colleagues, people we play sports with on weekends, etc. This is where the “too complex” part comes in: in FB, the network rigidly bins my connections into family, friends, friends of friends and everybody else. These are essentially fixed sets, concentric, that are more driven by privacy than anything else. In g+, the circles are supposed to be driven by interest rather than privacy. Stuff I’d like to share with my professional colleagues goes to the “bioinformatics” circle and/or the “science” circle. Personal stuff goes to “friends” or “family”. Like I said, this makes sense initially, because it follows our ideas of social interactions. But keeping people binned in your head, deciding who belongs where and who is privy to what information form which aspect of your life is something really fuzzy and complex. We do it every day, hopefully well, because we have been developing the social skills needed for compartmentalized communications since we were born. Just think back to the “paper published” situation. You want to inform your professional colleagues, family, maybe some closer friends, but your weekend running mates couldn’t care less. Except those two that you run with and are also scientists. Using FB you would just broadcast this information to all FB friends, and let those who care write comments on your post or wall. Supposedly g+ gives you a better option: post only to scientists, to friends, and family. But what about those two runners/scientists? OK, they may be also in your scientists circle but if they are not, that misses out. Compartmentalizing acquaintances in real life for information is complex enough, and I think that the g+ attempt to emulate this will not work well. This is where the “too simple” part comes in: to emulate your real-life compartmentlization, you need to perform dynamically complex intersections and deletions between those circles. Of course, doing this in real life is complex enough, and few, if any, would care to be bothered tweaking this on a social network for each and every post. Google+ circles is somewhat like the compartmentalization solution offered by FriendFeed rooms, but with a better interface.

What I foresee is a kind of facebook/friendfeed mashup. At most the average user will have handful of circles, with many messages going out to all where precision in targeting messages is sacrificed to ensure that all will get the message.

Oh, and nobody will give up Facebook quite yet, as inadequate as it is. So g+ should implement it’s FB and Twitter import/export plugins to draw in the crowds.

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