Work it!
I thought Instructables.com was pretty cool but now:
Evil Mad Scientists! How cool is that!
Everybody, get to work. Quick!
Evil Mad Scientists! How cool is that!
Everybody, get to work. Quick!
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22.12.07
20.12.07
WorldChanging: Changing the world?
It's amazing how mainstream being eco-friendly has become in the past few years. It is almost like if you want people to take action on something, you need to make it cool and sexy and marketable. take Worldchanging.com for instance. It has been around for a while and is getting more popular but I have to admit I only just stumbled upon it last week. At first I thought "cool, this looks like a great resource" but after perusing the site for a bit, I wasn't so excited anymore. For instance here is an article that obviously caught my eye: "Biomimicry Certificate Program". So of course when a Biologist thinks biomimicry, we think of poisonous butterflies. But hold on, biomimicry also means people literally mimicking biological processes. "Do you personally want to use biomimicry to redesign the world?" who can say no to that but can I believe that "...many people they have taught now teach biomimicry at universities, primary and secondary schools, and as consultants." well there are some very good points on the topic but I failed to see how it was immediately relevant to the average person looking to "change the world".
Anyroad, as you can imagine there is a book to go along with the site: "WorldChanging: A User's Guide for the 21st Century". But what do I really need to buy a book for? Here is an excerpt that is provided on the web page "In the middle of Denver, in the middle of December, you can walk into
most any supermarket and buy a ripe mango. This has been true long
enough that almost nobody stops to think of the remarkable distance
that mango traveled or of the tree it fell from, which is probably
enjoying a balmy tropical day on the other side of the planet.
Proponents of eating local food balk at the ubiquitous midwinter mango.
Why? Because they think about the baggage that mango flew in with." yeah, big surprise. Most conscience consumers realize these things. The title on that blurb is "Buy Local". Isn't that old news? As in "Think Global, Act Local"? Did everybody miss out on that in school?
I was curious as to what people had to comment about this book. Over at Amazon I found some very low ranking scores and one person recommended this book: "The Improving State of the World: Why We're Living Longer, Healthier, More Comfortable Lives on a Cleaner Planet" which is published by none other than the Cato Institute. Ironically Cato is something I found out about some months ago but have only started to dig into this past week. (Did I say I was busy in the lab? um, I meant I have lots of incubations). Baiscally, this book in the complete opposite of WorldChanging. So far, the point seems to be: "everything is great! Be Happy, Don't Worry!" Didn't I also hear that somewhere else before also?
Well I'm not sure how much of this Cato Institute I can support but their seminar "The Mind of the Market: The Case for Capitalism from an Evolutionary Perspective" should at least be entertaining. Oh, did I mention that Evolution is everywhere (but that doesn't mean anybody understands it). As for WorldChanging, I still have to wonder how much is really useful information vs marketing gimick, but if it gets people turned onto eco-friendly, there must be some redeeming qualities in there.
Anyroad, as you can imagine there is a book to go along with the site: "WorldChanging: A User's Guide for the 21st Century". But what do I really need to buy a book for? Here is an excerpt that is provided on the web page "In the middle of Denver, in the middle of December, you can walk into
most any supermarket and buy a ripe mango. This has been true long
enough that almost nobody stops to think of the remarkable distance
that mango traveled or of the tree it fell from, which is probably
enjoying a balmy tropical day on the other side of the planet.
Proponents of eating local food balk at the ubiquitous midwinter mango.
Why? Because they think about the baggage that mango flew in with." yeah, big surprise. Most conscience consumers realize these things. The title on that blurb is "Buy Local". Isn't that old news? As in "Think Global, Act Local"? Did everybody miss out on that in school?
I was curious as to what people had to comment about this book. Over at Amazon I found some very low ranking scores and one person recommended this book: "The Improving State of the World: Why We're Living Longer, Healthier, More Comfortable Lives on a Cleaner Planet" which is published by none other than the Cato Institute. Ironically Cato is something I found out about some months ago but have only started to dig into this past week. (Did I say I was busy in the lab? um, I meant I have lots of incubations). Baiscally, this book in the complete opposite of WorldChanging. So far, the point seems to be: "everything is great! Be Happy, Don't Worry!" Didn't I also hear that somewhere else before also?
Well I'm not sure how much of this Cato Institute I can support but their seminar "The Mind of the Market: The Case for Capitalism from an Evolutionary Perspective" should at least be entertaining. Oh, did I mention that Evolution is everywhere (but that doesn't mean anybody understands it). As for WorldChanging, I still have to wonder how much is really useful information vs marketing gimick, but if it gets people turned onto eco-friendly, there must be some redeeming qualities in there.
16.12.07
What is Life?
Erwin Schrödinger, 1944:
"How can the events in space and time which take place within the special boundary of a living organism be acocunted for by physics and chemistry? ...The obvious inability of present-day physics and chemistry to account for such events is no reason at all for doubting that they can be accounted for by those sciences."
"How can the events in space and time which take place within the special boundary of a living organism be acocunted for by physics and chemistry? ...The obvious inability of present-day physics and chemistry to account for such events is no reason at all for doubting that they can be accounted for by those sciences."
Chains and Networks (read Interconnectedness)
I was browsing around Amazon when I found "The Omnivore's Dilemma: A Natural History of Four Meals" on the New York Times best-sellers list for non-fiction. Here is an excerpt of a review from The Washington Post:
"...almost everything we eat has used enormous amounts of fossil fuels to get to our tables. Oil products are part of the fertilizers that feed plants, the pesticides that keep insects away from them, the fuels used by the trains and trucks that transport them across the country, and the packaging in which they're wrapped. We're addicted to oil, and we really like to eat."
"We've lost touch with the natural loops of farming, in which livestock and crops are connected in mutually beneficial circles."
These are great points and I am reminded of a Buddhist outlook on the situation. In the days of my M.Sc. I sat down to a wonderful home-cooked Indian meal from a friend of my roommate. The three of us plus another friend sat down to eat. We decided it would be appropriate to show our appreciation for the food and so each of us in turn said something (you can imagine the usual thanks offerings). When it was my turn I thanked the cook but also talked about the grocery store, the farmers, the transport companies, the employees of those companies, the truck manufacturer and their employees, the road and highway planners and those that maintain them, big gas & oil, and on and on. The point was that although our friend had prepared the meal there were countless people behind it, just like in every single thing we do everyday- none of us are independent.
If this book helps to get people to think about these topics more that will be a great feat and although I will probably never read the book, I have to be somehow glad to see such topics on the best-sellers list.
"...almost everything we eat has used enormous amounts of fossil fuels to get to our tables. Oil products are part of the fertilizers that feed plants, the pesticides that keep insects away from them, the fuels used by the trains and trucks that transport them across the country, and the packaging in which they're wrapped. We're addicted to oil, and we really like to eat."
"We've lost touch with the natural loops of farming, in which livestock and crops are connected in mutually beneficial circles."
These are great points and I am reminded of a Buddhist outlook on the situation. In the days of my M.Sc. I sat down to a wonderful home-cooked Indian meal from a friend of my roommate. The three of us plus another friend sat down to eat. We decided it would be appropriate to show our appreciation for the food and so each of us in turn said something (you can imagine the usual thanks offerings). When it was my turn I thanked the cook but also talked about the grocery store, the farmers, the transport companies, the employees of those companies, the truck manufacturer and their employees, the road and highway planners and those that maintain them, big gas & oil, and on and on. The point was that although our friend had prepared the meal there were countless people behind it, just like in every single thing we do everyday- none of us are independent.
If this book helps to get people to think about these topics more that will be a great feat and although I will probably never read the book, I have to be somehow glad to see such topics on the best-sellers list.
5.12.07
The Intellectual Entrepreneur
Another Bio article on salon.com, Craig Venter is the Future, more focused on the changing trends on how science is done:
"In the 20th century, the tenured professional supplanted the
independent gentleman scientist: James Watson succeeded Charles Darwin.
In the 21st century, the tenured professional is becoming outmoded,
replaced by the intellectual entrepreneur: The mantle is passing from
Watson to Venter."
In the end they conclude with a somewhat more comforting thought:
"In fact, Venter and his fellow intellectual entrepreneurs differ from
20th century tenured professionals most of all in their resemblance to
the researchers who the tenured professionals ostensibly eradicated:
19th century gentleman scientists, such as Darwin, who answered only to
themselves."
But although the tenure scientist is a different species to the "gentleman scientist" every professor I have met so far has a story that runs through all their research. I guess the fundmental difference is who they associate with.
"In the 20th century, the tenured professional supplanted the
independent gentleman scientist: James Watson succeeded Charles Darwin.
In the 21st century, the tenured professional is becoming outmoded,
replaced by the intellectual entrepreneur: The mantle is passing from
Watson to Venter."
In the end they conclude with a somewhat more comforting thought:
"In fact, Venter and his fellow intellectual entrepreneurs differ from
20th century tenured professionals most of all in their resemblance to
the researchers who the tenured professionals ostensibly eradicated:
19th century gentleman scientists, such as Darwin, who answered only to
themselves."
But although the tenure scientist is a different species to the "gentleman scientist" every professor I have met so far has a story that runs through all their research. I guess the fundmental difference is who they associate with.
Evolution Through Genetic Exchange
A colleague of mine mentioned a 'new' book on Hybrid speciation: Evolution Through Genetic Exchange (Michael L. Arnold). Acutally I found it came out in '06 (hardcover) but was recently released as a softcover. I was a little bit sceptical at first because it didn't really look like a hybrid speciation book, but those concerns are put to rest on the first page where Arnold points out that what he basically genetic exchange means hybridization. He begins by giving a brief treatment of the history of how hybridization (i.e. hybrid speciation) has been marginalized and/or disregarded by established post-synthesis evolutionary thought. Well I haven't finished reading it yet, but so far it's easy to read and I think pretty relevant to the new views on evolution and speciation being passed around. The downside is that the paperback costs an unbelievable 50EUR! Mann! I am getting the library to order this for sure.
4.12.07
Zotero
Zotero looks like a pretty useful plug-in for Firefox that helps to organize research projects while on the web. You can click on little icons in the url line and instantly add information to a database that is stored on your computer and hence available offline. You can also export all the information, including papers, for use in other programs.
1.12.07
The Testis as a Conduit for Genomic Plasticity
This has to be the coolest conference that I never heard about! Kudos to the organizers for publishing transactions, something that most other meeting are not involved in.
The Testis as a Conduit for Genomic Plasticity
The Testis as a Conduit for Genomic Plasticity
25.11.07
13.11.07
ID: Adapt and Assimilate
An interesting article in Salon.com today "The Evolution of Creationism". I like the puns, actually I spent the weekend watching borg episode of Star Trek (aside: ST ENT Borg are bogus!) and I can't help but see the similarities in the discussion of ID in this article and borg behaviour!
Stage 1: Adaptation
Defense: "Decades earlier, when the courts deemed creation science -- proto intelligent design -- a religious view and not constitutionally teachable as science in public schools,..."
Response: "....it adapted by cutting God off its letterhead and calling itself "intelligent design." "
Any good Borg Queen knows she need to adapt to the defenses of her prey in order to assimilate.
Stage 2: Assimilation
Strategy: " "We want to teach more about evolution," says Discovery Institute's Casey Luskin, "not less." The "more" they want to teach, of course, is what they see as evolution's shortcomings, leaving an ecological niche that will then be filled by intelligent design."
Well so far the assimilation has proven to be unsuccessful and just like the Borg splinter groups emerge:
Stage 3: Fragmentation
Strategy: "Creationist groups like Answers in Genesis, the Institute for Creation Research, and Reasons to Believe are now attacking I.D. for not having the guts to call its designer God or to be explicit about such key questions as the age of the world."
Ouch! Well you have Lore, Seven, Unimatrix Zero, so many problems to keeping a functional collective!
Damn Humanity and their Free thought!
Stage 4: Defense
Strategy: "the dogmatic Darwinists who have, the I.D.ers say, grown lazy and corrupt sitting atop a monopolistic theory with zero tolerance for dissent, within or outside of their ranks"
Well now, that's not true. There are at least three great books published in the last few years which deal heavily on different perspectives of Evolution:
1) Developmental Plasticity and Evolution (MJ West-Eberhard)
2) The Origins of Genome Architecture (M Lynch)
3) Evolution in Four Dimensions (E Jablonka, MJ Lamb)
Each has been recognized by the scientific community and have been recommended by various people as offering necessary and timly new perspectives in our understanding of Natural Selection and Evolution.
Resistance, it seems, in not futile.
Stage 1: Adaptation
Defense: "Decades earlier, when the courts deemed creation science -- proto intelligent design -- a religious view and not constitutionally teachable as science in public schools,..."
Response: "....it adapted by cutting God off its letterhead and calling itself "intelligent design." "
Any good Borg Queen knows she need to adapt to the defenses of her prey in order to assimilate.
Stage 2: Assimilation
Strategy: " "We want to teach more about evolution," says Discovery Institute's Casey Luskin, "not less." The "more" they want to teach, of course, is what they see as evolution's shortcomings, leaving an ecological niche that will then be filled by intelligent design."
Well so far the assimilation has proven to be unsuccessful and just like the Borg splinter groups emerge:
Stage 3: Fragmentation
Strategy: "Creationist groups like Answers in Genesis, the Institute for Creation Research, and Reasons to Believe are now attacking I.D. for not having the guts to call its designer God or to be explicit about such key questions as the age of the world."
Ouch! Well you have Lore, Seven, Unimatrix Zero, so many problems to keeping a functional collective!
Damn Humanity and their Free thought!
Stage 4: Defense
Strategy: "the dogmatic Darwinists who have, the I.D.ers say, grown lazy and corrupt sitting atop a monopolistic theory with zero tolerance for dissent, within or outside of their ranks"
Well now, that's not true. There are at least three great books published in the last few years which deal heavily on different perspectives of Evolution:
1) Developmental Plasticity and Evolution (MJ West-Eberhard)
2) The Origins of Genome Architecture (M Lynch)
3) Evolution in Four Dimensions (E Jablonka, MJ Lamb)
Each has been recognized by the scientific community and have been recommended by various people as offering necessary and timly new perspectives in our understanding of Natural Selection and Evolution.
Resistance, it seems, in not futile.
11.10.07
The Wonders of Creationism!
Jerry Coyne just sent these great clips around EvolDir.
I love 'em! Creationist don't need any help in looking stupid. I have to wonder where they come from 'cuz the second one looks too much like a spoof to be real.
I love 'em! Creationist don't need any help in looking stupid. I have to wonder where they come from 'cuz the second one looks too much like a spoof to be real.
26.9.07
Uprising in Burma
Probably everyone has already heard of the recent protests in Burma. Here are a couple links of the recent events from Spiegel Online on Monday and again today where shots fired at protesters, including monks are reported. The media has not started dubbing this the "Saffron Rebellion" I guess in keeping with the colour revolutions of Eastern Europe. I am really amazed that violent action is being taken against the monks. In Buddhist tradition harming a monk is akin to doing the same thing to your parents, it is really a loathsome act. Here are some other links:
You can sign a petition here, and keep up with breaking news at mizzima. Here is a video of interest. (Thanks to Jolanta and Bhante Ashin Sopaka at KBC for the links)
You can sign a petition here, and keep up with breaking news at mizzima. Here is a video of interest. (Thanks to Jolanta and Bhante Ashin Sopaka at KBC for the links)
Photo from Spiegel Online
25.9.07
Best Software for a Paperless PhD
I am now working on a super beautiful and fancy MacBook Pro that is provided by my chef (special shout out to the MPI-Evolutionary Biology).
there are lots of great MAC software for scientists. One good place to start is the Apple homepage for Science related software. There are plenty of great freeware things there.
Another great piece of software is the pdf manager called Papers developed by two dutch guys: Mek 'n Tosj. It's not freeare but you get a free 30 day trial and a 40% discount for students, which makes it a great bargain and it is certainly worth it!
There is a great tutorial about how to work with Papers and Net News Wire, a nice stand-alone RSS reader, which is also not freeware, but you can use it with annoyances without paying.
the other great software, which is freeware, is Journler, although it isn't marketed as an eLabBook it can certainly be used like one. I tried some of the Devon software but I didn't think they really did what I wanted for managing my files and eLabBook as a whole. Journler has the advantage of very easily putting in links to files on your hard drive. This is useful if you have lots of sequencing files or you ahve analyzed data and have the raw data plus that analyzed data in a folder. You can make an entry about that project/experiment and then make a link to the data which makes it much easier to find the software on your HD afterwards.
Another great piece of work I like is QuickSilver. This makes navigating around your harddrive and files alot easier. Although there are still some quirks I am happy with the rudimentary knowledge I have of the program. One thing I did was to make short cuts (apple+1 for firefox, apple+6 for papers, etc.) for all my frequently used programs. Then I don't have to see icons anywhere and they are even easier to access than clling up QS and typing in their names.
there are lots of great MAC software for scientists. One good place to start is the Apple homepage for Science related software. There are plenty of great freeware things there.
Another great piece of software is the pdf manager called Papers developed by two dutch guys: Mek 'n Tosj. It's not freeare but you get a free 30 day trial and a 40% discount for students, which makes it a great bargain and it is certainly worth it!
There is a great tutorial about how to work with Papers and Net News Wire, a nice stand-alone RSS reader, which is also not freeware, but you can use it with annoyances without paying.
the other great software, which is freeware, is Journler, although it isn't marketed as an eLabBook it can certainly be used like one. I tried some of the Devon software but I didn't think they really did what I wanted for managing my files and eLabBook as a whole. Journler has the advantage of very easily putting in links to files on your hard drive. This is useful if you have lots of sequencing files or you ahve analyzed data and have the raw data plus that analyzed data in a folder. You can make an entry about that project/experiment and then make a link to the data which makes it much easier to find the software on your HD afterwards.
Another great piece of work I like is QuickSilver. This makes navigating around your harddrive and files alot easier. Although there are still some quirks I am happy with the rudimentary knowledge I have of the program. One thing I did was to make short cuts (apple+1 for firefox, apple+6 for papers, etc.) for all my frequently used programs. Then I don't have to see icons anywhere and they are even easier to access than clling up QS and typing in their names.
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The Big Lie
Well somehow I am trying to get back into writing and maintaing a blog about all those aforementioned topics (see liner notes). So you see how below I make that promise of more frequent posts? ja, well tht didn't really happen, but let's just say lots of things were happening lately.... more posts to come. I promise :)
Oh, and now you can see this ScribeFire link at the bottom of my posts because that is what I am using to post now. I think it's pretty nifty so I don't mind the link there.
Oh, and now you can see this ScribeFire link at the bottom of my posts because that is what I am using to post now. I think it's pretty nifty so I don't mind the link there.
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13.8.07
The Wonderful World of Macs
I received my new MacBook Pro the other day and have been enjoying looking at all the great apps that I missed out on while using the clunky Dell PC I began my studies with. My favourite so far is Papers, a pdf reference manager. It works kinda like iTunes, but for journal articles. There are a couple of bugs but it makes sorting through your journal articles much nicer. And also I am loving Quick Silver, I'm just getting used to it but so far it has treated me well.
More frequent posts and more science soon I promise.
26.6.07
The Summer of Statis and PopGen
I'm taking a great statistics course right now. Great mostly because it's available, we get into more juicy stuff in the weeks to come (It's going veeeeerrrrrrry slow, and today only myself and two others showed up for it). I came across a great web application to do analysis until I get SPSS installed on my system. It was not hard to find but nice nonetheless, and I like the attention-grabbing headline:
Web pages that perform statistical calculations!
Another resource I will be checking out is the new popgen toolbox for MatLab.
12.6.07
The Summer of Art
So, as I return from an extended haitus, and hopefully back to discussing my favourite science topics. I begin again with some exciting art fairs that are happening in Europe.
The obvious big draw (and the most expensive) is the Venice Biennale, incorporating art, dance, theatre and music. Actually I would love to go, depends on how cheap I can get tickets for Venice.
One artist presenting her work is London's Tracey Emin (above) whose work will focus on abortion and sexual abuse of children. I saw a great exhibit of hers in Amsterdam a few years ago and I really enjoyed it. She is able to mix in a great deal of personal matter into her work and be very upfront about it. She is the focus what she is showing as much as the message.
Two other very exciting event are happening very close-by. One is the 12th Documenta in Kassel. This is pretty exciting and I've heard about it for a while, it's so close that it is definatly doable.
The last one is the Skulptur Projekte Münster a giant outdoor sculpture festival that happens every 10 years and is even close than Kassel. Perhaps it is not even worth to just spend the time at the local exhibits than having to go abroad.
6.3.07
The Lord's Encyclopedia
I should know enough to not bother, but somethings are just to unbelievable to be true.
From Spiegel Online:
Wikipedia for Christian Fundamentalists
How you call something based on ignorance and outright bias any kind of encyclopedia (see Conservapedia and CreationWiki) is beyond me, but at least you know to take everything with satire right from the onset.
You don't have to look long to find erronous. From CreationWiki:
Evolutionism is the belief(1) in the theory that life on Earth is simply the result of random, natural processes, and ultimately attempts to explain the existence of humans by means other than divine creation(2).
1) Evolution is not a faith, no belief is required. In fact if scientists told you to simply believe them, nothing would get published. Those kinds of scientists don't last long.
2) Science is not concerned with proving things for the purpose of negating religion. They may find it depressing to hear that Science is actually not concerned with Religion, the relationship is a bit one-sided.
Is there some hope? Well at least EvoWiki has been up and running for some time, and for anyone who is willing, there is a multitude of information discussing what Evolution actually is, and is freely available though libraries, online and open access journals.
3.3.07
PersonalDNA
If you ever thought that DNA wasn't useful enough, welcome to your personalDNA.
So apparently I'm an Animated Creator:
- You are outgoing, comfortable with others, and up for anything, which makes you ANIMATED
- Your imagination, confidence, willingness to explore, and appreciation of beauty make you a CREATOR
Bio Machines
Yesterday I heard a good, and information filled, talk by Dustin Penn, a mainstay in the MHC world. He described analyzing the scent of families in secluded Swiss villages. One point was that it was not possible to distinguish familial from nonfamilial individuals. The point of technological thresholds came up in the discussion period and Penn of course pointed out that a dogs nose is much more sensitive than the best machines available to chemists today. I thought, but isn't that why we're Biologists then?
New Millennium Evol'n
Here an interesting older review that I stumbled across: James A Shapiro: A 21st Century View of Evolution: Genome System Architecture, Repetitive DNA, and Natural Genetic Engineering. It describes new ways of thinking "about genomes as sophisticated informatic storage systems and about evolution as a systems engineering process"
From an organizational point of view, distant effects of repetitive element dosage tell us that the whole genome is a single integrated system, regulated both in cis- and trans- by networks employing DNA repeats.
The emphasis here on repetitive DNA means to take into account centromeric and telomeric regions, and other dispersed repeats (which contain signals for transcription, chromatin organization and nuclear localization of DNA itself. That's a big portion of the genome that is included in this. While a number isn't given for this classification, transposable elements, which are most likely included here, comprise 40% of the human genome (and more of the mouse) alone. In other words, we are talking about a huge amount of the genome that has a role in regulation. Regulatory evolution just got a whole lot bigger- and messier.
Another interesting point:
...bioinformatics is far more than the application of contemporary technology to large data bases. Bioinformatics has the potential to lead us to novel computing paradigms that may prove far more powerful than the Turing machine-based digital concepts we now use.
There are many different analogies people have tried to use to make sense of biological systems. At the end of the day they all fall somewhat short. One of the things this statement is eluding to is that thinking about biological systems on their own terms is the best way to understand them. There is not analogy that can summerize fundamental biological processes.
The most exciting point for me is:
Significant evolutionary changes can result form altering the repetitive elements formatting genome system architecture, not just from altering protein and RNA coding sequences.
In other words, understanding genome architecture is fundamental to understanding Evolutionary changes and part of the key lies in repetitive elements. This and many papers that have been published since point to the declining emphasis of SNPs in evolutionary study and a shift to other sources of (random) variation.
28.2.07
Quote of the Day
Barbara McClintock, 1980, re: Transposable Elements
"Since the types of genome restructuring induced by such elements know few limits, their extensive release, followed by stabilization, would give rise to new species or even genera"
via A. Fontdevila
24.2.07
Genomania! Book-a-rama!
Michael Lynch has a new text book coming out next month. It's called The Origins of Genome Architecture and is published by sinauer and Associates (who also have some other great science titles). Briefly:
Under Lynch’s hypothesis, the genome-wide repatterning of eukaryotic gene structure, which resulted primarily from nonadaptive processes, provided an entirely novel resource from which natural selection could secondarily build new forms of organismal complexity.
By nonadaptive processes I think they are refereing to drift and mutation and how these two random processes interact to provide the material for Natural Selection.
An important point to keep in mind when thinking about Natural Selection is that it is at least a two-step process. The first, random stage (where drift and mutation come into play) is where all the variation is generated that in the second, nonrandom stage are eliminated (i.e. survival of the fittest). I look forward to a treatment of organismal complexity with regards to drift and mutation.
You can get a feel for what is to come with a recent review in Science: Mutation Pressure and the Evolution of Organelle Genomic Architecture.
Another book that I want to try and tackle soon is West-Eberhard's Developmental Plasticity and Evolution. Although I have heard great things about it, it doesn't seem to be a very accessable (i.e. easy to get into) book.
And also, a potentially interesting textbook on Evolution by CSHL comes out this summer, but who know if it offers anything about what is already available (but the webpage sure is nice).
The RNA Intermediate
I came across this great paragraph in Principles of Population Genetics by Hartl (3rd ed):
The central role of RNA in gene expression is one of the oddities of biology taht makes sense in the light of evolution. That gene expression is configured around RNA is a legacy of the earliest forms of life when RNA molecules served both as carriers of genetic information and as catalytic molecules. The role of RNA as carriers of genetic information was gradually replaced by DNA, and the role of RNA as catalytic molecules was gradually replaced by proteins. At every step along the way, as the RNA world evolved into the DNA world, the role of RNA was indispensable in the processes of information transfer and protein synthesis, and so the RNA intermediates became locked in place.
An apt summation of the idea. An interesting aspect is that indeed RNA still does retain it's catalytic capabilities (i.e. regulatory) in many organisms and also it serves as information storage in many viruses, and there is even some evidence of that role in plants. So despite the ancestry of this division of labour, RNA still seems to maintain it's "ancestral" roles, and is not simply an intermediate between DNA and protein. I wonder what the future holds in terms of DNA as catalytic and protein as information storage. Perhaps some findings will change the dogmatic views of the roles of these molecules also.
23.2.07
Danger
Today was the last day for the Annual Spring Meeting here in Cologne. The topic this year was "Evolution on Immunity and Pathogens". The two most exciting talks for me were from Max D. Cooper who presented an exciting model of adaptive immunity in agnatha which is quite distince from that in the gnathostomata. The other exciting talk was an overhead talk (as is typical) by Polly Matzinger discussing her Danger Model of Immunity and her adamant debunkment of traditional views into immunology.
20.2.07
The Gay Allele
There was an interesting News and Views published last month in Nature. This piece discusses a paper by Gravrilets and Rice in PNAS outlining population genetics models of how a genetic basis for homosexuality would be maintained in a population.
The problem:
Homosexuality has a cost to fitness — that is, the ability of an individual to produce offspring that survive and reproduce — and it can only evolve if it otherwise provides indirect benefits to reproduction.
The models:
First, in the case of overdominance, a 'gay allele' would result in homosexual behaviour in an individual who has received this allele from both parents (homozygous), but would provide an advantage to the heterozygote
In the second case, sexually antagonistic selection, a gay allele would result in a cost when expressed in males ('feminization' and loss of fitness), which would be counterbalanced by a fitness advantage when it is expressed in females.
In the third hypothesis, kin altruism, homosexuals would help their own family members, increasing the fitness of their relatives and therefore the probability that a gay allele is passed on to the next generation.
The paper itself goes on to discuss models for the first two scenarios, however the major assumption stands:
a gay allele will produce variable degrees of homosexual behaviour, which is equivalent to the fitness cost of that behaviour
This gives a very skewed image of the phenotypic penetrance. In an allele whose phenotype can be covered up it is difficult to make such assumptions as to the correlation between a gene and the extent of the phenotype. You could make a case that social acceptance gives a better correlation to sexual behaviour than genetic factors, if they were ever found.
The last model, which is not discussed in the paper, is also interesting. The classic example of kin altruism is among eusocial insects, however, humans are certainly far from the model of eusociality. worker ants are either prevented or unable to concieve (by parthenogenesis) or to mate unless the conditions allow it. Such a strong distinction between reproducing and non-reproducing castes do not exist for humans.
The News and Views makes a good point about the importance of this paper in that "it generates several testable predictions". It would seem more interesting to investigate homosexual behaviour in nonhuman animals, where unbiases perspectives are more likely.
13.2.07
Wandern
"Wandern" is the German word for "hiking", but when I hear it I can't help but think of wandering. Well, depending on who you go with with hiking really is a lot like wandering.
I like the idea of wandering thou. It reminds me of the wonder that surrounds me. I'd prefer to wander through my ideas, books and papers instead of getting directly to the point right away. At least in those cases where I have time my prefered method is to read a paper and stop at some point, even after the first sentence, and begin to daydream about what I just read. Then I'm off! Wandern! It's usually at these times that I come across the most exciting conclusions and connections to other things I have read.
The idea of wandering though life also fascinates me. I remember reading "Memoirs of a Geisha" (on the very trustworthy recommendation from Oprah). In in the protagonist talks about her water sign and how her life is a reflection of a path of water flowing through a river, it's path bending and guided by the many features surrounding it, constantly changing, moving. In a sense the water just flows, it flows because it flows, always travelling, moving, wanderning through the river. In Buddhism the River comes up when talking about emptiness and impermanence. What is the river? can you touch the river? By the time you see the river and think about it, it is gone. There is no river, it is constantly changing. This is a starting point for a reflection of ourselves. We are the river, constantly changing and moving, there is no real thing that is the person. You can't grab it and call it a person, and in that sense we are rivers and we are wandering. Thorugh forests, life and ideas.
It is also an apt description of evolutionary direction. There is no direction to speak of (although there are, of course, constraints). Mutations act at random, drift acts at random. The collective influence of stochiastic events is incredible. And so it is not just the individual that wanders but it is indeed a reflection of all of nature.
12.2.07
Good Morning, Charles. Good Night, God.
What could be a better day to begin a science blog than on Darwin Day.
Yes folks, today marks the 198th birthday of the grand daddy of Natural Selection. The very name Darwin still ignites excitement in the hearts of many, scientists and religious folk alike, but for very different reasons.
To be honest, I am a bit disgusted at the use of religion as a political weapon but by the same token, I can't agree with people using science to argue with religious institutions. You can find any number of blogs praising evolution and Darwin and in the same breath having utmost contempt for religion.
Perhaps the thing I find most ironic of it all is: Dogmatic religious attitudes are condemned by most of the science establishment, yet their convinction of Darwin and their contempt for religion is in itself dogmatic.
This is my favourite quote about relgion from a scientist:
Buddhism has the characteristics of what would be expected in a cosmic religion for the future: It transcends a personal God, avoids dogmas and theology; it covers both the natural and spritual; and it is based on a religious sense aspiring from the experience of all things, natural and spiritual, as a meaningful unity. -Albert Einstein
That, in short, is what it's all about. I hope to develop this blog into a home for my thoughts and observations on the exciting aspects of my scientific life as well as highlighting the inherent compatibility of science, nay life, with Buddhism. Not ever post will deal with both, or even either.
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