Sarah Palin – Jonathan Eisen's Lab

Palin announces opposition to research on Homo sapiens

Sarah Palin today has followed up her attack on fruit fly research by condemning much of the NIH Budget and a variety of other scientific earmarks. At a town hall meeting yesterday while campaigning in Guam, Palin said

“We asked federal agencies to give us a summary of key words relating to research projects and we found an enormous number of them focused on homosapiens. I kid you not.”

When asked by a teenage audience member to explain what was wrong with this research Palin said

“You probably are a homosapiens no? Or have many friends that are? What we need to do is spend money on helping people change and not on studying these homosapiens”

The teen tried to respond but was escorted forcefully out of the hall by security while Palin continued on in her meeting. At the end of the meeting Palin returned to the topic of science research and said “If elected, the McCain-Palin ticket will reallocate federal funds to eliminate waste on topics like homosapiens and fruit flies. Enough is enough.”

McCain Palin going after fruit flies

As if scientists did not have enough reasons to vote against McCain-Palin who seem to have decided that Bush was overly supportive of science. Now Palin is attacking of all things “fruit-fly research.” Lovely. Proof that they are both clueless (not knowing what a fruit fly is probably) and anti-science at the same time. For more on this see:

Sarah Palin’s Still Dangerous Views on Teaching Evolution

Well, Palin has clearly revised her public position on teaching evolution. In part of her interview with Katie Couric it was addressed (I got the transcript here. )

Couric: Do you believe evolution should be taught as an accepted scientific principle or one of several theories?

Palin: Oh, I think it should be taught as an accepted principle. And, you know, I say that also as the daughter of a school teacher, a science teacher, who has really instilled in me a respect for science. It should be taught in our schools. And I won’t ever deny that I see the hand of God in this beautiful creation that is Earth, especially coming from one of the most beautiful states in the Union and traveling around this country also in this last month. My goodness, just seeing, you know, the beautiful landscape of New Mexico recently. That was just breath taking and seeing the rolling hills in Virginia and all … the beauty that is this Earth, I see the hand of God in that. But that is not part of state policy or a local curriculum in a school district. Science should be taught in science class.

Sounds promising right? I mean, previously, she seemed to be wishy washy on the separation of science and religion and now she seems to be trying to do the right thing. But just when you might have thought the anti-science part of her was winning out, look at her response to the next question:

Couric: Should creationism be allowed to be taught anywhere in public schools?

Palin: Don’t have a problem at all with kids debating all sides of theories, all sides of ideas that they ever – kids do it today whether … it’s on paper, in a curriculum or not. Curriculums also are best left to the local school districts. Instead of Big Brother, federal government telling a district what they can and can’t teach, I would like to see more control taken over by our school boards, by our local schools, and then state government at the most. But federal government, you know, kind of get out of some of this curriculum and let the locals decide what is best for their students.

This basically follows the script of the Intelligent Design supporters who have been pushing for changes in the education curriculum by local school boards. And it is pretty dangerous in my mind. There should be separation of church and state. Period. At the federal level. At the state level. And at the local level. And this is clearly an attempt to circumvent that concept. So – Palin is ~~towing~~ toeing the ID line here pretty closely and who knows ~~who~~ what havoc she would wreak on science in this country if she were elected. McCain-Palin is starting to look more anti-science than Bush-Cheney, hard as that is for scientists to imagine.

See my earlier post on Palin and evolution here.

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.

Sarah Palin on EvolutionCreationism

Well, it seems McCain has further embraced an anti-science agenda with his pick as Sarah Palin as his running mate.

The Science Bloggers are a bit up in arms over this. I think there is some hope that she/McCain will drift back to the middle on this at some point but they both now seem to fall in the camp of the Intelligent Design supporters. It is the “independent” streak both do seem to show occasionally that gives me hope that if they do get elected, they will not be as tied to the ID supporters as they will be during the election.

Anyway, here are some things I found on the web about Palin’s evolution views:

NewMiner.Com: in response to written questions in a 2002 election …

Q: The education section of the Republican Party of Alaska’s platform states “We support giving Creation Science equal representation with other theories of the origin of life. If evolution is taught, it should be presented as only a theory.” Do you support this position? Why?

A: I support this plank in the Republican Party’s platform. I believe society can have healthy debates on scientific theories, so equal representation of creation and evolution shouldn’t be an offense.

Anchorage Daily News in 2006 reported

The volatile issue of teaching creation science in public schools popped up in the Alaska governor’s race this week when Republican Sarah Palin said she thinks creationism should be taught alongside evolution in the state’s public classrooms.

Palin was answering a question from the moderator near the conclusion of Wednesday night’s televised debate on KAKM Channel 7 when she said, “Teach both. You know, don’t be afraid of information. Healthy debate is so important, and it’s so valuable in our schools. I am a proponent of teaching both.”

Most other thigns I have seen are rehashing these two stories in some way. If anyone has any other detail I would love to see it.

Examples of blog posts on this issue include: