system biology link

http://www.nature.com/reviews/focus/systemsbiology/index.html

Wizard Inheritance

นักวิทยาศาสตร์จากออสเตรเลีย (Royal children hospital, Victoria, Australia) พยายามเอาแฮรี่ พอตเตอร์มาสอนเด็กให้รู้จักพันธุศาสตร์

เพราะเขาบอกว่าจากเนื้อเรื่องของแฮรี่ พอตเตอร์ พ่อมดเป็นชนกลุ่มน้อยที่แอบปะปนอยู่ในกลุ่มมักเกิ้ล(ผู้ไม่มีเวทย์มนต์)

ทีนี้ สิ่งที่น่าสนใจก็คือพ่อมดแม่มดจะเป็นชนชาติใดก็ได้ อาจจะเป็นลูกหลานของผู้วิเศษหรืออาจจะเป็นลูกหลานของพวกมักเกิ้ล หรืออาจจะเป็นลูกครึ่งที่เรียกว่า half blood ก็ได้เช่นกัน

ลองมาดูการวิเคราะห์ของเขากันครับ
เขาว่าคุณสมบัติผู้วิเศษ(Wizarding abitily) จะสืบทอดต่อกันทางพันธุกรรมตามกฎของเมนเดล (บาทหลวงปลูกถั่วอ่ะ)
ทีนี้ ถ้าจำบทเรียนเรื่องเมนเดลกับถั่วลันเตาลือชื่อของแกได้จะรู้ว่าแกใช้สี ลักษณะผิวเมล็ดและลักษณะอื่นๆ ของถั่วของแกในการคิดเกี่ยวกับการถ่ายทอดทางพันธุกรรม

อ้าวแล้วทีนี้ ลักษณะอย่างหนึ่ง (เราเีรียกฟีโนไทป์) ก็ขึ้นกับตำแหน่งบนโครโมโซมที่เรียกว่าอัลลีล
หรือพูดง่ายๆ ก็คือยีนนั่นแหละ

เอาล่ะ ทีนี้พูดกันง่ายๆ ก็คือไอ้เจ้ายีนที่ว่าเนี่ยมันก็มียีนเด่นกับยีนด้อย
คนหนึ่งคนจะมียีนเนี่ยอยู่สองก๊อปปี้ อันนึงมาจากพ่อและอีกอันมาจากแม่
ขอแค่มียีนเด่นแค่ก๊อปปี้เดียว คนนั้นหรือไอ้ตัวนั้นก็จะแสดงลักษณะเด่นออกมา

เอาล่ะ ทีนี้เจ้าคุณสมบัติของผู้วิเศษเนี่ยมันเป็นยีนเด่นหรือยีนด้อยกันครับ?
คำตอบก็คือยีนด้อย

ทำไมล่ะ?

ก็ลองคิดดูสิครับ
ถ้า Wizard allele (W) เป็นถูกข่มด้วยลักษณะเด่นของ Muggle allele (M)

อย่างที่บอกไว้ข้างต้นว่าทุกคนมีสองก๊อปปี้
อันนึงจากสเปิร์มของพ่อ (W or M) และจากไข่ของแม่ (W or M)
เพราะงั้น permutation ที่จะเป็นไปไ้ด้ก็จะมี

W (sperm) + W (egg) = WW
W (egg) + M (sperm) = WM
W (sperm) + M (egg) = WM
M (sperm) + M (egg) = MM

ถ้า M (muggle = dominant หรือยีนเด่น) และ W (wizard = recessive หรือยีนด้อย)
ทั้ง WM และ MM ก็จะกลายเป็นมักเกิ้ลทั้งหมด

ในขณะที่ WW จะกลายเป็นผู้วิเศษ

จากสมมติฐานนี้ จะได้ว่า

Ron Weasley, Neville Longbottom และ Drago Malfoy เป็นพ่อมดเลือดแท้ที่มาจากสายเลือดพ่อมดทั้งหมด
หมายความว่าพ่อแม่ของวิสลีย์ ลองบัตท่อมและมัลฟอย มียีน WW ทั้งหมด เพราะงั้นทั้งสามคนก็เลยมียีนเหมือนกันคือ WW ทั้งหมดเลยกลายเป็นพ่อมด

แฮรี่ ถึงแม้ว่าทั้งพ่อและแม่จะเป็นพ่อมด (WW ทั้งคู่) แต่แม่ของแฮรี่เิกิดในตระกูลของมักเกิ้ล ซึ่งหมายความว่าคุณตาและคุณยายของแฮรี่เป็น WM ทั้งคู่ เพราะงั้นทั้งตาและยายของแฮรี่จึงเป็นมักเกิ้ลในขณะที่คุณแม่ของแฮรี่ได้รับยีนด้อยมาจากทั้งสองคนคือ WW จึงกลายเป็นผู้วิเศษ

เฮอไมโอนี่ ก็อยู่ในกลุ่มเดียวกับแม่ของแฮรี่ซึ่งก็เกิดมาจากมักเกิ้ลเหมือนกัน แต่เป็นมักเกิ้ลที่เป็น WM ทั้งคู่ เฮอไมโอนี่เลยได้ WW มาเลยกลายเป็นผู้วิเศษไป

ทีนี้ ในกรณีของซีมัส เพื่อนอีกคนของแฮรี่ ซึ่งเป็นเลือด half blood มีพ่อแม่เป็น WW และ WM เลยกลายมาเป็นผู้วิเศษเหมือนกัน

แต่ก็มีข้อที่น่าสนใจอย่างเช่น เนวิล ลองบัตท่อมที่ไม่ค่อยจะเก่งในเรื่องของพ่อมดแม่มดเท่าไรทั้งๆ ที่เกิดในตระกูลพ่อมดแม่มดหรือพวก Squib ที่แม้จะเกิดในตระกูลพ่อมดแม่มดแต่ไม่มีึความสามารถของผู้วิเศษอาจจะเกิดจากการกลายพันธุ์ในยีน WW ที่เขามีทำให้สูญเสียหรือทำให้แอคติวิตี้ของยีน (ที่ทำให้เป็นผู้วิเศษ) ลดลงไปก็ได้

ผมอ่านแล้ว นิยมในความคิดของการนำเรื่องราวที่เด็กสนใจมาช่วยทำให้การเรียนรู้ทางวิทยาศาสตร์ดีขึ้น
(เมื่อไรครูไทยจะทำได้งี้มั่งเนีย?)

Ref :
Jeffrey M. Craig, Renee Dow and MaryAnne Aitken, Harry Potter and the recessive allele Nature 436, 776 (11 August 2005)

Another Flat Earthism?

The Darwinism, theory that is more like a core of the evolutionary biology where most of the tenets in the field have been relied on for more than 150 years, is now being ruined from a group of christian scientists who believe in supernatural creation or so-called "intelligent design" aka ID. Why ?? because the darwinism is contradict to what bible says about god creation.

Despite many strong evidences and experiments supporting modern evolution theory, Many extreme arguments is still being raised against it. What are their arguments?
Some scientists or activists, as someone called them, had tried to illustrate the unlikeliness of evolutionary biology by calculating probability and possibility of the development of such a complex system like an eye. Of course, finally they concluded that it is implausible that the natural complex system like eye could indeed be developed from such a really simple system like chemical mixing and evolutionary stuffs without guiding from some supernatural intelligence or what they call "designer". Mere mutations and natural selections would not be enough to accomplish that level of intricacy. However, such calculation has not been published in any general accepted peer-review journal.

Well! then another question arises "where are the designer from?" ... No answer has been made for now !!

Another argument would be "Do we have enough information to precisely calculate the probability of an eye development like that they claimed they do? if not will we be able to use this calculation as a reference?". At least, Harvard professor of mathematics and evolutionary biology, Martin Nowak doesn't think that according to knowledge we have so far, it would not be feasible to accurately predict the probability of an eye came about hence this calculation seems wacky.

Well! There is no conclusion at this point. As a matter of actual fact, many people try to correlate this 2 theory together. At the same time, many try to support either one of them. Unfortunately, many just have fun watching the conflicts as for amusing themselves after work T_T.

One may ask what should we believe? Well IMO, at this point I do believe in the evolution theory because there are more evidences indicating its validity. And there is an inevitable Achilles's heel of intelligent design which is there is no way to neither conduct the experiment supporting the idea nor to proof it. Moreover, there are plenty of evidences supporting the evolution theory and many more to come!

Why is this quacky issue is matter?.. The point is what side should the school teach children? Should they talk about god creation or not talking about it at all.

As for me, I found this topic interesting because I don't see the point where the argument should be originated from anyway. Why don't they just simply add all of the reasons supporting both sides in to the curriculum so that the kids get to know both theory and they can finally use their own judgement to evaluate which one they want to believe.

The flat earthism idea can still be taught in school together with the sphere model of earth by Galileo Galilei. The Copernicus hypothesis also have been taught without any problem with the idea of earth is a center of the universe! Well!! the funny part is that they believe that there are turtles carrying earth.

Well! Anyway, theory can be replace by the new if in case there is some other strong evidences are discovered! All we need to do is just open our mind and we will do just fine ..

don't you think ?


More info :
1. Claudia Wallis, The Evolution wars from TIME magazine Issue August 15, 2005
2. http://en.wikipedia.org/wiki/Intelligent_design
3. http://www.discovery.org
4. http://www.talkorigins.org/faqs/darwinism.html
5. many books about dawin's theory

Math Lesson

Unbelievable, I have been struggling with basic mathematic like probability and stuff. It seems that it is important to me to learn all these things if I really want to pursue my career in the field of Biophysics. I cannot avoid studying it anymore no matter how much I hate calculation.
Well! It has been a long time since my last math course. I have not been making much progress for my study. Indeed, I am not productive at all.

After 3 days of excruciating study! I have finished the first chapter in a book so-called “Molecular Driving Forces” and have started to think more reasonable. At least, that is what I feel (optimistically). Anyway, I surely got some gist of what probability is and how important it is in Statistical mechanics calculation of biological system.

so pathetic, isnt it?

Streptavidin rocks again!

Streptavidin is one of the most well understood ligand-protein binding complex. It is naturally composed of 4 separate chains arranged into 2 dimers. The attempt to make a stable single chain dimer of streptavidin for amendability to phage and chip display has long remained unsuccessful because of the streptavidin binding site is made up of portions of both dimers therefore when the tetrameric complex is disrupted, the biotin binding pocket is lost.

Charle Cantor and his group in Boston University, MA just discovered a really interesting story about the mutant streptavidin dimer in that despite significant reduction in biotin binding affinity, the mutant is able to bind B4F (biotin-4-fluorescein) at 100000-fold higher than the ability to bind biotin.

Moreover, though the B4F binding is at a very high affinity, it is reversible unlike the traditional streptavidin-biotin system that binds very tightly so that draconean condition will be required for releasing of biotin.

Reference:

1. Allison D, Nature Methods 2005 July 22;2(8):573
2. Aslan FM, Yu Y, Mohr SC, Cantor CR.,Proc Natl Acad Sci USA. 2005 Jun 14;102(24):8507-12.
   

synthetic biology

cool

some more interesting stuff

http://www.sciencemag.org/sciext/125th/
http://www.biomachina.org/
http://www.ub.rug.nl/eldoc/dis/science/
http://www.ph.tn.tudelft.nl/Courses/FIP/noframes/fip-Contents.html
http://nramm.scripps.edu/
http://nramm.scripps.edu/seminars/2003/cryoem/lectures/
http://www.yaleglobal.yale.edu/
http://www.yaleinsider.org/
http://us.expasy.org/
http://saturn.med.nyu.edu/research/sb/stokeslab/image-analysis.html
http://its.med.yale.edu/software/mac/powerpoint_files/logo_listings2.html
http://partners.adobe.com/public/developer/opentype/afdko/topic_feature_file_syntax.html#1

Cyberman

After a long period of terrible insomnia. Today I have had a damn good rest all day.

I start writing an article in Thai again about the Cyborg. Indeed, It is such a pain in the ass to do something I haven't done for at least 5 years.

Cybernetic organism is something really interesting. I never know that this technology exists in a matter of 30 years by a pioneer in the field of wearable computer and, of course, cybernetics, Steve Mann, after the term was coined by Manfred E Clynes and Nathan Kline in 1960 in the NASA human space exploration.

Mann start wearing his machine 25 years ago and he live his life with it most of the time. In 2002, he was confiscated by the airport security in Canada and was enforced to remove his cybernetic setup. By which, He was having problem with nausea and many symptoms so he had to board on the wheelchair like a handicap. It is pretty obvious that he has integrated himself to the technology far too intimately and far too long. Therefore he, ultimately, cannot endure separating from it anymore.

Mann's invention is actually really interesting. His eyetap is capable to freeze moving object like wheel of running car or rotating propeller of a plane. Moreover it can record still image of what he is looking at at his whim.Stopping object from moving gives him an opportunity to have better face and detail recognition as well as ability to see something he cannot visualize clearly with his natural eyes. His wearable computer ,in addition, augments his remembrance by giving him extra-memory where he can access it anytime he would want to when it is attached to his body.

Well! Even though some people think he is just another blasphemist who is trying to enhance his ability to against god, he is still continue doing his amazing and extraordinary works and hope that one day it might change the way of our life to the better direction.

Big picture

Discussion with Fenny is always intellectual and interesting.
Having been discussing with many people always taugh us something at least how they think.

Fenny reccommend me a book so-called "A PhD is not enough" by Peter J Feibelman.

The first chapter is about how to deal with the project and assignment and so on.

We were discussing part of this book espectially how to see the big picture of the whole project we have to do, what is the goal and what is the way to achieve that goal.

We have also finally come to the conclusion that, usually, if we ask people about the technical detail of how to conduct our work from some experts without telling them the outline or the big picture of the work itself, they are not going to be interested and, usually, they will not pay attention on whatever we are asking even though it is a total match on their expertise. This might be because of the fact that they don't see how important the work is to them or they dont really know exactly what the question is...

Anyway, I found a review of this book byDerek R. Oliver, Ph.D

" 1 - "Do you see yourself in this picture"In the preface, Feibelman describes the development of young scientists as a " ...Darwinian selection process ..." based on "benign neglect." With this assertion in mind, he describess a number of case histories that illustrate various intellectual, structural and iterpersonal "traps" that exist in the early (PhD/postdoc) stages of a science career. These examples are brief enough to so that the reader doesn't lose the overall thread of the chapter, yet contain enough details that the cases illuminate the points being developed.Emphasis is placed on the need for an aspiring scientist to find a mentor to over come the "neglect" mentioned in the preface. The choice of such a person leads into some of the aspects of the next Chapter."

Well! I think I will need to read this book myself to be able to say something more.

A Ph.D. Is Not Enough: A Guide to Survival in Science by Peter J Feibelman

Book review : http://scijobs.freeshell.org/c-derk.htm

Shaker structure revealed

my gosh! Shaker K channel is humongous, Rod Mackinnon rocks again.
According to his new duopapers with Steve Long in Science, The shaker type Kv1.2 Potassium channel structure has been solved down to 2.9 A resolution which also give us some glim of how the voltage gated potassium channel works.

The contradiction of the sensor movement is in a very big argument. I just waded through his papers a couple times without really concentrating myself reading them.

However, the structure is really beautiful and the crystal packing seems to have a lot less contraint than the KvAP. Even if Steve add back the magic mixture of lipid into the crystal trial, the final structure doesnt show any density of the lipid at all which will leave a mystery if the crystal packing still effects the transmembrane part of the protein becasue of

1. There is a tremendous space between the pore domains in the crystal which is likely to be filled with lipid However, this may not be a big issue because it is also possible that the lipid itself is too fexible to be able to resolved any structure by diffraction.
   
2. The pore domain still interact with Beta region of another Kv1.2 channel which may somehow distort the orientation of the flexible helices in the crystal but this shouldnot be a problem either.

Well! this structure indeed give us an enormous information about the eukaryotic potassium channel and provides a lot of insight into the movement of the voltage sensor of the famous Shaker channel.

All I could say is that "his work is always extremely impressive"

Gelernter & Silver Sand Beach

Originally, we planed to go canoeing. Unfortunately, we cannot find launch point so we went back to VA hospital where my friends work.

A friend of mine told me about his advisor.I found out that his PI's brother is very famous computer professor who has been contributing significantly in parallel computing (esp. in tuple space) and developing of Linda programming system.

After the glorious day, Prof Gelernter got a mailbomb by Unabomb who was identified as "Theodore Kaczynski" former mathematic Asst Prof at UC Berkeley.

Fortuitously, Prof. Gelernter is still alive. Even though he suffers from the permanent damage with his right hand and eye, Still he published a book "Drawing Life: Surviving the Unabomber" and was, subsequently, nominated to be and finally become a member of National Council on the Arts. In addition, he is now a seminal contributors of the rightist magazine (rightist are referred to the right-wing, the political right in left-right politics)

Finally, we stop by the Silver Sand Beach in Milford for unintentional sunbathing and picnic. It was fun even if I got darker by -2 according to photographic grayscale.

Anyway, after all, I then look up more about Unabomber. I found that there are many more intelligent mathematical killers other than Kaczynski.

The Zodiac (a.k.a. serial killer) is another remarkable one. He/She had continuously killed people by knife and shortgun in the full moon night and remains unidentified even if he left a bunches of clues and ciphers.

Right after I went home to rid all my carry on, I went to Starbuck to have coffee where I was impressed by a fine drawing of a local artist. We had had some chat about art and life and I was shock after realizing that he has some problem with bipolar disorder.

My goodness! Despite his psychological problem, this guy has potential in arts. That tells me one thing; you cannot judge people from their station and blah blah...

At The Beginning

Beginning my blog in english. I don't know how much time I will be spending on this but we shall see anyway

Deep in thought

I just found a really interesting paper in Nature (436, Jul 2005) saying that the

"Cybernetics thingy just jumps into psychiatry business."

Neurosurgeons in Catholic University of Leuven in Belgium and in University of Cologne, Germany have individually successfully employed the technology so-called DBS or Deep Brain Stimulation which basically is a type of implantation of a stimulator into chest or belly of the patient where they can control it remotely. The stimulator is connected to several microelectrodes which are inserted into an extremely precise neuroanotomical target in the brain to help normalizing neuronal activities of the problematic neuron in Obsessive-Compulsive Disorder (OCD) patient.

It is amazing how they actually visualize the brain (fMRI) and make a tomogram (Positron Emission Tomography) and finally pinpoint where exactly to put electrode to stimulate the brain. The team originally believe that the high frequency pulse from stimulator merely block excitatory neuron, by which, it damp down all the circuit. Low frequency does the same but by stimulating the inhibitory neuron instead.

Another cool stuff after having heard about implant of the first real cyborg guy "Matt Nagle".

Whewww !!