Misc. – Page 158 – Jonathan Eisen's Lab

Tracing the evolutionary history of Sarah Palin: links to a parasitic nematode and the pathogenic fungus Botryotinia fuckeliana

You see, as a total sequence analysis dork, when I see names, I frequently ask whether the letters in the name include only letters which are used as amino acid abbreviations. I started this game when the brilliant notes/letters came out in Science in the early 90s about whether ELVIS was overrepresented in protein sequences. Of course, despite being 20 years old, Science still keeps these under wraps requiring registration to see them (see for example the Stevens letter).

Anyway, alas, three of the major candidates for the US election have names that do not use traditional amino acid abbreviations so I am stuck with analyzing Sarah Palin. But that is OK because of her professed aversion to evolution and support to Creationism (and since sequence analysis is inherently an evolutionary study).

So – I took here name and went to the NCBI Blast page and did some searches. And what came up? Well, here are some of the top hits from the blastp searches (which I used to compare the pretend peptide “SARAHPALIN” with all the peptides in the non redundant collection at Genbank).

>ref|XP_001545292.1|  hypothetical protein BC1G_16161 [Botryotinia fuckeliana B05.10]
gb|EDN25226.1|  predicted protein [Botryotinia fuckeliana B05.10]
Length=383

GENE ID: 5425746 BC1G_16161 | hypothetical protein
[Botryotinia fuckeliana B05.10]

Score = 26.9 bits (56),  Expect =   189
Identities = 8/9 (88%), Positives = 8/9 (88%), Gaps = 0/9 (0%)

Query  1    SARAHPALI  9
            SARA PALI 
Sbjct  209  SARAQPALI  217

>ref|YP_061725.1|  homoserine dehydrogenase [Leifsonia xyli subsp. xyli str. CTCB07]
gb|AAT88620.1|  homoserine dehydrogenase [Leifsonia xyli subsp. xyli str. CTCB07]
Length=451

GENE ID: 2939000 thrA | homoserine dehydrogenase
[Leifsonia xyli subsp. xyli str. CTCB07] (10 or fewer PubMed links)

Score = 26.9 bits (56),  Expect =   189
Identities = 8/9 (88%), Positives = 8/9 (88%), Gaps = 0/9 (0%)

Query  1    SARAHPALI  9
            SAR HPALI
Sbjct  267  SARVHPALI  275

>ref|ZP_02031476.1|  hypothetical protein PARMER_01474 [Parabacteroides merdae ATCC
43184]
gb|EDN87136.1|  hypothetical protein PARMER_01474 [Parabacteroides merdae ATCC
43184]
Length=299

Score = 26.1 bits (54),  Expect =   340
Identities = 7/8 (87%), Positives = 8/8 (100%), Gaps = 0/8 (0%)

Query  3    RAHPALIN  10
            RAHPAL+N 
Sbjct  170  RAHPALVN  177
>ref|XP_567332.1|  hypothetical protein CNJ01520 [Cryptococcus neoformans var. neoformans
JEC21]
ref|XP_773201.1|  hypothetical protein CNBJ1950 [Cryptococcus neoformans var. neoformans
B-3501A]
gb|EAL18554.1|  hypothetical protein CNBJ1950 [Cryptococcus neoformans var. neoformans
B-3501A]
gb|AAW45815.1|  hypothetical protein CNJ01520 [Cryptococcus neoformans var. neoformans
JEC21]
Length=437

GENE ID: 3254188 CNJ01520 | hypothetical protein
[Cryptococcus neoformans var. neoformans JEC21] (10 or fewer PubMed links)

Score = 26.1 bits (54),  Expect =   340
Identities = 8/9 (88%), Positives = 8/9 (88%), Gaps = 0/9 (0%)

Query  1    SARAHPALI  9
            SAR HPALI 
Sbjct  415  SARQHPALI  423

>ref|YP_001626035.1|  citrate synthase [Renibacterium salmoninarum ATCC 33209]
gb|ABY24621.1|  citrate synthase [Renibacterium salmoninarum ATCC 33209]
Length=386

GENE ID: 5822379 RSal33209_2898 | citrate synthase 
[Renibacterium salmoninarum ATCC 33209]

Score = 25.7 bits (53),  Expect =   456
Identities = 9/11 (81%), Positives = 9/11 (81%), Gaps = 2/11 (18%)

Query  1    SARAHP--ALI  9
            SARAHP  ALI 
Sbjct  218  SARAHPYAALI  228

>ref|YP_001817256.1|  integral membrane sensor hybrid histidine kinase [Opitutus terrae
PB90-1]
gb|ACB73656.1|  integral membrane sensor hybrid histidine kinase [Opitutus terrae
PB90-1]
Length=936

GENE ID: 6208547 Oter_0366 | integral membrane sensor hybrid histidine kinase
[Opitutus terrae PB90-1]

Score = 25.2 bits (52),  Expect =   611
Identities = 7/7 (100%), Positives = 7/7 (100%), Gaps = 0/7 (0%)

Query  3    RAHPALI  9
            RAHPALI 
Sbjct  256  RAHPALI  262

>ref|YP_001757871.1|  putative anti-sigma regulatory factor, serine/threonine protein
kinase [Methylobacterium radiotolerans JCM 2831]
gb|ACB27188.1|  putative anti-sigma regulatory factor, serine/threonine protein
kinase [Methylobacterium radiotolerans JCM 2831]
Length=331

GENE ID: 6141303 Mrad2831_5232 | putative anti-sigma regulatory factor,
serine/threonine protein kinase [Methylobacterium radiotolerans JCM 2831]

Score = 25.2 bits (52),  Expect =   611
Identities = 7/8 (87%), Positives = 8/8 (100%), Gaps = 0/8 (0%)

Query  2    ARAHPALI  9
            ARAHPAL+
Sbjct  299  ARAHPALV  306

>ref|ZP_01466013.1|  hydrolase, TatD family [Stigmatella aurantiaca DW4/3-1]
gb|EAU63211.1|  hydrolase, TatD family [Stigmatella aurantiaca DW4/3-1]
Length=209

Score = 25.2 bits (52),  Expect =   611
Identities = 7/7 (100%), Positives = 7/7 (100%), Gaps = 0/7 (0%)

Query  3   RAHPALI  9
           RAHPALI 
Sbjct  79  RAHPALI  85

>ref|YP_001558323.1|  glycosyl transferase group 1 [Clostridium phytofermentans ISDg]
gb|ABX41584.1|  glycosyl transferase group 1 [Clostridium phytofermentans ISDg]
Length=357

GENE ID: 5743305 Cphy_1206 | glycosyl transferase group 1
[Clostridium phytofermentans ISDg]

Score = 25.2 bits (52),  Expect =   611
Identities = 8/10 (80%), Positives = 8/10 (80%), Gaps = 0/10 (0%)

Query  1    SARAHPALIN  10
            S RAHP LIN 
Sbjct  113  SERAHPLLIN  122

There does not appear to be a perfect match in the NCBI NR protein database. But take a close look at the #1 scoring hit. That is right, it is from and organism called Botryotinia fuckeliana. No comment on the appropriateness of this name, but it does contain a term I will probably use a lot if she gets elected.

Of course, anybody who has heard me blather on and on about evolution knows that I am always talking about how blast top hits are not a good measure of relatedness per se (see my NAR paper where I first talked about this in 1995). So – I decided to build a tree of Sarah Palin. I used the NCBI Distance Tree option which you can do from blast searches.

Since most likely you cannot see that in enough detail – here is a zoom in.

That one did not come through on the Blog so well either so I decided to output the tree in Newick format and then I searched for a program that could draw a better figure on the web (we have tools in my lab to do this but I am trying to do this all on the web as an exercise). And I found a web site that makes drawtree available. And I plugged in the Newick format and it made a nicer one.

Though making trees from really short sequences is not ideal, in this tree, Sarah Palin is shown to be at the root of a branch including a protein from the parasitic nematode Brugia malayi. So if we take an evolutionary interpretation it seems that this causative agent of filariasis (well, a protein from this agent) is descended from SarahPalin. In other words, she seems to be ancestral to this parasite.

So in conclusion – by similarity – SarahPalin is closest to a plant pathogen with an unusual name. And by phylogeny SarahPalin is ancestral to a parasitic nematode. Sounds about right.

Help save the world and get $100,000 seed grant to do it

Just got this email and thought I would share since it does relate to some of the themes of my blog. I note that the Gates Foundation is VERY supportive of Open Access publishing as one of their previous grants helped support the journal “PLoS Neglected Tropical Diseases.” I am hoping that at some point the Gatges Foundation will require OA publishing for all of the projects they fund.

The Bill & Melinda Gates Foundation is now accepting grant proposals for Round 2 of Grand Challenges Explorations, a US$100 million initiative to encourage unconventional global health solutions.

Based on your feedback, we have made changes for Round 2 of Grand Challenges Explorations. We modified the topics from Round 1 and added two additional topics. We will no longer require applicants to register for a topic in advance of submitting their proposals. We also updated the application form in response to feedback from the initial round.

Grant proposals are being accepted online at http://www.gcgh.org/explorations until November 2, 2008, on the following topics:

New! — Create new vaccines for diarrhea, HIV, malaria, pneumonia, and tuberculosis
New! — Create new tools to accelerate the eradication of malaria
— Create new ways to protect against infectious diseases
— Create drugs or delivery systems that limit the emergence of resistance
— Create new ways to prevent or cure HIV infection
— Explore the basis for latency in tuberculosis

Initial grants will be $100,000 each, and projects showing promise will have the opportunity to receive additional funding of $1 million or more. Full descriptions of the new topics and application instructions are available at http://www.gcgh.org/explorations.

We are looking forward to receiving innovative ideas from scientists around the world and from all scientific disciplines. Anyone can apply, regardless of education or experience level. If you don’t submit a proposal yourself, we hope you will forward this message to someone else who might be interested.

Thank you for your commitment to solving the world’s greatest health challenges.

Quick Post – Spore Sounds Cool

Nothing conclusive here. I have not tried it yet. But Spore sure sounds like a cool evolution game to play. See Carl Zimmer’s NY Times article and his blog for more.

I see PLoS in everything III: PLoS Hats

Thanks to my mom for this one. PLoS Hats rule.

Cool Plant Comparative Genomics Resource: Phytozome

I spent the last few days at a “retreat” for the Joint Genome Institute and heard about a few things there worth sharing with everyone. I will try and post about some of them in the next few days. Here is one. The JGI and the Center for Integrative Genomics have made a pretty cool tool for comparative analyses of plant genomes. It is called Phytozome and has a variety of simple and nice features. JGI is doing more and more work on plant genomes as part of their energy research and I think Phytozome could turn into a good place to go to get the latest plant genome information. Go to http://www.phytozome.net to see the real thing.

I see PLoS in everything #2

OK – I cannot help it. Whenever I see this little train letters in stores everywhere I spell something related to PLoS. If you support OA, please continue the conspiracy and spell something OA-related wherever you find letters like this. PS – Vaughn this is for your kid.

Redefining Tomorrow’s Table

Tony Trewavas has an interesting review (Redefining “Natural” in Agriculture) in PLoS Biology of my friend and colleague Pam Ronald’s new book “Tomorrow’s Table: Organic Farming, Genetics and the Future of Food.”

I was planning on eventually writing my own review of her book but not sure when I will get to it. I personally like the book a great deal, and enjoy how it switches back and forth between the authors (Pam and her husband Raoul Adamchak) and how it interweaves personal stories with discussion of the science and practice of organic farming and plant genetic engineering.

Trewaras has some things in the review I agree with a great deal like

“The text deals with many of the questions raised by the public about GE crops in a sensible and balanced manner, quoting various sources of reliable information on the concerns about risks to health and environment that often recur. It also mentions Richard Jefferson, who is Chairman of CAMBIA, a non-profit organisation that attempts to make the tools of biotechnology widely and freely available (http://www.cambia.org/). As a scientist, I cannot help but applaud!”

I personally love what CAMBIA is doing and found the discussion of CAMBIA in the book to be interesting. I have gotten to know Richard Jefferson over the last few years and think he is a true pioneer in revolutionizing biotechnology and freeing it from the shackles of over protectionism.

Trewavas also has a very interesting thread about the value of different opinions. Since this was printed in PLoS Biology and is under a CC license I can reprint it here (with acknowledgment of the source – Citation: Trewavas T (2008) Redefining “Natural” in Agriculture. PLoS Biol 6(8): e199 doi:10.1371/journal.pbio.0060199) and it is worth doing so:

The continuing conversation did not resolve the issues between them. It convinced me, however (if I needed convincing), that while everyone is entitled to their opinions, when dealing with detailed technical matters of science or medicine or any subject that requires enormous qualifications and experience, the notion that all opinions have equal validity is simply downright wrong. If you want real information on the safety of heart surgery procedures, do you follow the advice of a qualified heart surgeon or the local butcher? If you want advice on flying a jumbo jet, do you ask the local bus driver or a pilot with 10,000 hours of experience flying jumbo jets? And if you want advice on how to captain a supertanker, do you ask a person whose experience is limited to rowing a dinghy? Mistakes by surgeons are not uncommon, 70% of air crashes result from pilot error, and occasionally supertankers hit the rocks. But relying on rank amateurs instead of professionals would guarantee instant catastrophe. Many branches of science are very complex. However, being a scientist isn’t enough, of course, as being a scientist doesn’t qualify you to advise on any subject except your specialty. To provide advice that can lead to sensible policy requires not only a thorough understanding of the workings and literature of the particular scientific area but many decades of experience in that field.

It is unfortunate that for the past 40 years, agriculture in particular has been damaged by opinionated groups of the public that have forcefully used fear and anxiety and carefully selected information to try and coerce policy makers to adopt their own mistaken and unqualified views. Fear and emotion do not make for good policy. I applaud Ronald’s conclusion that “if citizens vote, it should be for a specific matter on which they are well informed, not because of general concerns about a new technology.”

The corollary is that on most technical matters, the public can never be well enough informed. If scientific knowledge does not form the basis of policy on technology, basing such policy on ignorance can be guaranteed to generate disaster. It was Slovik in his classic Perception of Risk [3] who demonstrated that non-experts overestimate the frequency of death from rare causes while underestimating the frequency of common causes of death, and who established clearly how additional knowledge changed expert understanding. The use of the local ordinance by activist groups to stop GE farming is only too reminiscent of the damage done by Lysenkoism to Soviet farming in the 40s, which took decades to recover from, once it was abandoned.

Basically, he is indirectly agreeing with Ronald/Adamchak that some negative opinions of GE are simply not valid. Here I think I disagree with all of them. I think much of the objection to GE modification of plants is an esthetic objection and thus presenting scientific arguments for why it is OK to do is a bit off tangent. It is kind of like when someone says “that house is ugly.” Do you respond by saying “Well, actually, the shape and color patterns have been shown to appeal to human sensory systems” Not too helpful. I feel that the same is happening with GE plants — if people’s instinctively do not like them, telling them about the science is not necessarily going to help. Nothing wrong with educating about the science, but I think it is a red herring to say that some of the anti-GE folks do not understand the science and therefore their objections must be wrong. I feel similar vibes in the evolution education discussion going on around the world. I think many people latch on to ID and Creationism because it appeals to them in a esthetic sense. And one needs to be really gentle/careful about bringing science into the discussion (except of course, when one is teaching a science class — then you teach the science).

So sure – I have some quibbles about parts of the book. As does Trewavas (he has to raise some objections – any book review that does not have them seems like fan mail and not a review).

Despite my quibbles here and there, the book really is a must read for those interested in GMOs and/or the organic farming movement as well those thinking about “slow food” and other related topics. In addition it is a wonderful personlized story, with a mixture of recipes, stories of research, discussions of teaching about organic agriculture, and some minor family drama. For the same reason that I like Amy Harmon’s New York Times stories (such as the recent one on evolution) I like this book – it personalizes what is frequently a boring impersonal discussion.

And of course it does not hurt that the heart of the story / discussion is good. Ronald/Adamchak present an overall idea I have a hard time arguing against – GE and organic growth practices both have a lot to offer the world and if we took the good parts of both, a “GE-Organic” system might be highly beneficial to all. For example, in principle, GE plants can lead to a reduction in the use of pesticides and fertilizer. Similarly, they could lead to a reduction in water use and higher crop yields. Since it seems unlikely that the current organic movement will embrace the benefits of GE crops, it will probably require a whole new movement to merge the two. It will also require the companies and organizations that push GE to do it with the environment and health of people and the planet in mind. To me, the biggest problem with GE food and farming is that it seems to be used more to help the farmers and the companies selling stuff than the consumers and the public. If that changed, I can see people embracing GE plants in much the same way they embrace GE medicines.

PS – For more on the book see Pam’s blog here.

Twisted Tree of Life Award #1: Salk Institute Press Release on Kinases

I am starting a new award here — for people or sites that do something silly in regard to the “Tree of Life” but should know better. That is, this is for scientists or sciency sites that do something unseemly with the Tree of Life. And the first award goes to the Salk Institute for their press release relating to a paper on kinases in single celled choanoflagellates (OK – the pres release is a month and a half old but I was out sick – and I drafted this 7/8/08). In the press release, which discusses a PNAS paper by Gerard Manning and colleagues (Manning does some really great comparative work on kinases and helped me look at kinases in a few genomes such as that of Tetrahymena thermophila). I note – it seems Manning or someone has paid the OA fee for this paper so anyone can read it.

The paper seems both sound and interesting. And it has a really really cool tree figure.

But the press release has a few doozies. The worst (or best, I guess, depending on your point of view) is the following:

It commands a signaling network more elaborate and diverse than found in any multicellular organism higher up on the evolutionary tree, researchers at the Salk Institute for Biological Studies have discovered.

Yup that is right. A modern organism, living today is somehow “lower” on the tree of life than we are. Too bad the person who wrote the press release did not read Amy Harmon’s recent Times story on evolution education. Or they could have gotten help from the high school science teacher Harmon featured, who taught his students about how modern organisms did not evolve from other modern organisms.

And for using one of my most hated metaphors in all of evolution (higher and lower organisms), Salk gets my first “Twisted Tree of Life Award”

Building a new Alvin

Quick post here. For those interested in Deep Sea research, you should check out the story by William Broad in the NY Times on building a replacement for Alvin (New Submersible to Expand Deep-Sea Exploration). Alvin is a wonderful little submarine that I and many others have relied upon for much of our research. But it definitely has some issues. And it looks like Woods Hole Oceanographic Institute is in the processof building a replacement.

Tree of Life Imagery at Starbucks

Not the best resolution (damn that iPhone camera) but just thought I would post the picture I saw at a Starbucks in San Francisco where I was for a DARPA meeting discussion the “laws of biology”. You see – even Starbucks is a fan of the Tree of Life.

——————————————

Follow up. After Laura wrote in asking about the origins of this picture I have searched around and found many others interested in it. I note – the caption says “The Deeper the Roots – the Higher the Reach”. I have not found the origins of the print but here are some other discussions

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