Foldings of A Curious Mind

My journey to Lindau Nobel Laurate Meeting

2010-06-25T19:30:00.003+06:00

Time flies by!

Last couple of months were kind of hectic for me with SwapnoJaatra! Its nice to have a break!

Four or five months back, I got this chain email from one of my subscribed group that the Lindau Council at Bangladesh asked for online application from interested individuals for Interdisciplinary Lindau Nobel Meeting 2010. I was hesitant initially. Fortunately, for me, Mustak bhaya insisted that I should apply. I had two days in my hand (the last date was knocking at the door :p). Collected all the documents and applied. There has been a number of steps, initially I was selected from Bangladesh, then I had to apply at the Lindau Committee.

I think it was sometime around May! I got this email from the Lindau Committee congratulating me for being selected! That's a WOW!

Time passed by, required documents started to come to us (Me and Tania apu). Then an email came asking for application from those individuals who are interested to attend EUROSCIENCE OPEN FORUM 2010 @ Torino, Italy meeting after Lindau Conference. I thought, why not? But I wasn't sure about this one, 40 to be selected out of 650! It was a pleasant surprise at the end, I was selected based on my write-up!

Two weeks of Europe tour: 1 week @ Lindau, Germany and 1 week at Torino, Italy.... the journey has just began!

My laptop is running out of its battery charge :( There is no option of plugging power cable at Dhaka Intl Airport, I guess I've to stop now!

Conscious learning at Vegetative state!

2009-09-21T15:50:00.004+07:00

As mentioned in one of my previous posts, I'm not a fan of neuroscience per se, but I find deep interest in human psychology and cognition. Its only interest though, I've not yet done my home-works on these subjects!

I first read about the condition in New Scientist, its been a while... (may be I took that issue from Chittagong British Council which means it was at least 4 years back!) The article was patients who lost their motor function, yet have unaffected sensory perception. I wish I could do something for them. Being trapped inside the body and no communication with the world around you... its hard for me imagine how it feels! But we, the human being, survive.

The issue is closely intertwined with the patients in vegetative state, as declared by doctors. In a recent research, it was revealed that some of the patients in this state have their conscious learning part intact and their ability of conscious learning correlates with their prospect of recovering later on. This is an interesting result indeed. I would recommend reading the following link:

http://www.scientificamerican.com/article.cfm?id=learning-in-vegetative-state

After 19 days... Jackson still going strong in charts

2009-07-13T22:14:00.005+07:00

I was checking out this week's last.fm chart, Micheal Jackson at the top: expected. But the way he was leading... most loved, top artist, top track, even in hyped track (some of the less famous tracks of Michael)... hyped artist included Jacksons and Michael's brother Jermaine!

10 Apple top album includes 3 Michael ones!

19 days and still leading all the charts, I don't buy the conspiracy theories, but at least Michael's sister La Toya Jackson is literally right, "He was worth more dead than alive."

Moving my 360 blog to wordpress

2009-07-04T20:31:00.005+07:00

Yahoo 360. Once it was part and parcel of my life; Apart from serving as a diary which bears marks of the history of certain part of my life, I had 81 friends, a huge fan base and more than 22000 web visits. Unfortunately yahoo has decided to shut down its 360 service on 13th July 2009. Like most of the fans of this service, I'm utterly disappointed. But at the end, I'd no choice but migrate my blog to other platforms.

There were many options, at least according to Yahoo!

Migrate to yahoo profile
Migrate to wordpress, blogger or other platforms

Couple of google searches and I myself found following additional options:

Import tool at My Opera
Import tool at Multiply

Yahoo profile seems okay, the only problem is I couldn't find the comments! Besides no image, no html imports. Only texts being imported. Its disappointing. I tried with blogger, but failed due to absence of any sort of import option!

All of the rest three imported part of my blog!!!

Wordpress imported without the images.
My Opera imported only the comments.
Multipy imported only the blogs, leaving the comments behind.

It felt like yahoo willingly ignored its 360 users! Considering all these facts, I opted for wordpress, manually added all the images (wasn't easy with 125 posts!) and tags. Now its in shape, at least to some extent.

The social networking face is missing from wordpress, but at least I've the blog!

I kept the weblink similar to my 360 one!

http://neelsky2000.wordpress.com/

How language shape our cognition

2009-07-03T15:09:00.001+07:00

Apart from Molecular Biology, there are certain other subjects on which I've deep interest. Psychology, Cognitive Neuroscience (unlike some of my peers who are quite enthusiastic about the subject, I'm not a fan of general Neuroscience) as well as Linguistics. While going through my google reader updates from wordorigins, I ended up in this page on How does our language shape the way we think?

This is quite an informative review on the interface between human cognition and linguistics! Clearly described and well reviewed. Some facts discussed are indeed worth pondering.

Anyone interested in human language development and its effect on shaping our thoughts and emotions should give a look!

I've already hyperlinked to the web-page, in case you couldn't find, the link is given below:
How does our language shape the way we think?

Nature, Science and Michael...

2009-06-26T22:14:00.005+07:00

It has been a long day :p Slept a lot, the only productive part of it was going through the current issues of Nature (Volume 459 Number 7250 pp1033-1160) and Science (Volume 324 Number 5935 pp1603-1754).

If you're reading Nature or Science, definitely you're going to find something interesting, no matter what is your taste or interest. Anyway, to me, current issues of both of the journal lacked the usual glamour, generally I cant pick my clear favourate. One article in Science really caught my attention, the group assayed DNA-Protein interaction of ~100 mice Transcription Factor (TF) DNA Binding Domain (DBD); Vol 324 p 1720. Another paper on formation of functional centromere by synthetic heterochromatin was worth mentioning; Vol 324, p 1716.

Nature was slightly better, there were three articles on science journalsim which I thought worth reading; Vol 459, pp 1054-1057. The research article on membrane fusion (p 1091) and correlation between transcription and DNA replicatio fidelity (p 1150) was quite interesting. But I thought the paper on role of mechanical force generated by the first cardiac pump in embryonic haematopoesis is a masterpiece (p 1131).

Last but not least, I woke up this morning and my brother gave me this bad news: The King of Pop Michael Jackson died of cardiac arrest. The news was really a saddening one, but we all have to die at some point of time.

Heal the world... Make it a better place... for you and for me and for the entire human race... RIP Michael.

Repairing XP Boot file

2009-06-24T19:39:00.005+07:00

About an hour ago, my sister came to me complaining her XP doesn't start! It gives an error message which roughly says it can't find boot file at C:\Windows location. Right then I knew its a mess, definitely the boot.ini has been deleted. So I asked what happened? The initial story was, there was load shedding, when power supply resumed and the PC was tried to turn on, the message kept on appearing. Then she said, she wrote this code yesterday which deletes files and it deleted lots of files in C: drive and she thought its no big deal since the OS is installed in E: drive. By then I figured out whats wrong, I replied although the XP is installed in E: drive, the boot file is in C: drive and now the PC can't find the boot file, thus no start up.

Anyway, despite my initial thought this would be a tough task, it turned out to be an easy one! I used XP installation CD, selected repair option, then typed \help in the command prompt, there was help on command \bootcfg, I knew I was in the right place, I used the \rebuild command, I didn't understand some of the queries of the command, so googled and came up with this about.com article, a handy one, which solved my problem. Below is the link:

Repair or Replace boot.ini file in Windows XP

I thought I might share in case anyone faces similar problem.

DST from my perspective

2009-06-20T21:00:00.010+07:00

The country is clearly another step ahead by using DST, Daylight Saving Time, from tonight. I wont go for justifications (one of my friend, Minhaz seriously doubts its any positive effect and he put forward lots of geographical explanations, lets not go to that.)

What I felt is the government failed to publicize it. Its now just a high class educated society clock time change phenomenon, rather than being an event of mass participation. I can give an example form my own life. The guard at our house today refused to open the gate at 7 am, he was insisting the gate will be opened at 7 but now its only 6 am. My brother, to his utter annoyance, failed to convince him that 7 is 7 and all the offices, schools, colleges and universities will start according to the new time schedule.

But the fact is, I'm not surprized at all, its the way things work in our beloved country. We have some highly talented individuals at the administration who execute their decisions without even the need of planning, let alone the concept of proper planning. Its ridiculous to start DST when technically we have already finished summer and on the brink of the longest day of the year (21st June, DST should be evenly distributed at the both side of the longest day, i.e. if DST is in operation for two months, one should be before the longest day, the rest should be after it).

Hail us and our leaders...

Image courtesy:
http://pakistaniat.com/images/Daylight-savings-Time.jpg

Catching Cold by reading New Scientist !!!

2009-01-03T21:43:00.002+06:00

Theoritically right now I should not be writing blogs, I should have been checking different universities or taking rest :p

Anyway, couple of days back I was reading this article on Common Cold in New Scientist I brought from British Council. It was kind of interesting. Three suggestions were there if you want to avoid cold (don't sue me if you still catch cold):

Avoid direct contact with children, they are miserably efficient in transmitting viruses.
Avoid having cold feet, I'm not quite sure how this works, but I think the mechanism is if your feet is cold, the blood flow is directed to feet reducing the flow at the nose, thus reduced immunity! (No reference please, I'm not quite sure about the mechanism myself)
Finally, wash your hand regularly. In case you shake your hand with a person who has cold, you can also catch! Wash them, be safe :)

The funny thing is after reading the article, I wasn't feeling that much good! The very next day I caught cold! Is there any mechanism of catching cold by reading New Scientist article on Common Cold :p

Evolution of Anthocyanin pathway gene dihydroflavonol-4-reductases

2008-07-01T05:59:00.002+06:00

I've started writing reviews of recent papers on GNOBB. I'll post my reviews here also. Below goes my first review, its on gene evolution through duplication, published online in Nature.

Gene duplication is one of the major ways of evolving genes with novel functions. There are two models on how gene duplications lead to new functions: 1) The NEO-F Model (Neo-functionalization) & 2) EAC (Escape of Adaptive Conflict) Model. In NEO-F model, new function is achieved after the event of duplication. On the contrary, in relatively unexplored EAC model genes acquire novel function which maintains its ancestral function also. This gene is constrained from improving either novel or ancestral function because of detrimental pleiotropic effects on the other function. But upon duplication, any of the copies can be selected for enhancement of the novel function. In a recent paper accepted in Nature Marias et al. explores the evolution of Anthocyanin pathway gene dihydroflavonol-4-reductases (DFR, EC number 1.1.1.219) in Eudicots with respect to both of these models. Their study suggests EAC as mode of evolutionary change of this gene. Besides they also conclude EAC may be far common mode of evolution than previously thought. One interesting conclusion of their study is that the evolution of novel function may sometimes be a byproduct of the evolution in enhanced ancestral activity.

Ref: Marais et al (2008). Escape from adaptive conflict after duplication in an anthocyanin pathway gene. doi:10.1038/nature07092.

Sequencing Beta-Globin

2008-03-06T10:49:00.002+06:00

Yesterday our Thalassaemia research has crossed an important milestone, it may be a small step in our project yet it is the very first and utterly significant stride towards achieving our ultimate goal.

We have successfully sequenced a region of Beta-globin from a healthy individual. We don't yet have the sequence in our hand, expecting to have it in a while. I'm quite excited!!! Can't wait anymore....

DNA at last

2008-01-17T01:29:00.000+06:00

Last few days had been quite hectic, starting from the 1st Day of 2008.

The objective was isolation and amplification of 587 bp region of Beta-globin. Started with isolation of buffy coat. I think this was the trickiest step, required lots of anticipations and assumptions. But I think we're very lucky, it didn't take much of our time. Then the DNA isolation and PCR. Today we've successfully completed PCR.

I'm very excited about tomorrow's work!

HFE stands for Haemochromatosis

2007-08-12T22:53:00.001+06:00

Actually I should have posted this blog at least four months earlier...

Our bioinformatics assignment had a part on Haemochromatosis gene, its nomenclature HFE appeared bit confusing, so I had searched for its origin. Well, there was no specific answer but I got something.

The actual reason behind naming this gene as HFE is not known, but FE might be for Iron, which is closely associated with the pathogenesis of this disease. Some scientific literature states this gene as HLA-H, eventhough there is a wide debate in designating this gene in the group of HLA (Human Leukocyte Antigen).

Reference:
Hemochromatosis gene nomenclature; American Journal of Medical Genetics 93:77 (2000)
www.genenames.org/activities/publications/PMID10861687.pdf

Scientific or Promotional!!!

2007-04-06T17:44:00.001+06:00

Today a scientific conferance on Promotion of Biotechnology in Bangladesh: National and International Perspective has started at Sasaka Auditorium, ICDDR,B. The official URL for the conferance is

http://www.promotebiotechbd.net/index.htm

I was going through the conference schedule and related stuffs. My first reaction was, "Actually what is the purpose of arranging this conference?"

Its not a scientific conference. Most of the papers and posters going to be presented are already published stuffs!

A conference to promote biotechnology? Neither. In fact it will do even worse if this is the purpose. Only 300 restricted participants... inside a closed auditorium... no interaction with general people.

Another thing irked me. There is a cultural function session! Doesn't make any sense. To make things even worse Shuvro Dev has been paid Tk. 50000 to perform. Waste of invaluable money and time. You don't need cultural functions in scientific conference...

Bangladesh is a weird country with strange peoples! A conference has been arranged for the sake of arranging a conference... no goal, no objective...

Dream or Myth

2007-02-05T21:23:00.000+06:00

BAS told not to disclose to anyone.

He thinks he knows someone who can cure cancer ... any type !!!

A dream or A myth!!!

Well, lets wait and see ;)

My 2nd Year Bioinfo Report

2007-02-03T21:08:00.000+06:00

We have to write a report on Bioinformatics project each year.

Here goes my 2nd year bioinformatics report. (Course: GEB 207)

The Journey From Sequence to Structure.

Restriction Enzyme

2007-02-02T20:53:00.000+06:00

Restriction enzymes are important tool for molecular biologists. As far as I know, these enzymes are solely found in Prokaryotic System... Is there any Eukaryotic Restriction Enzyme?

If you know any, please put the name and its source in the comment box.

Enjoy your time.

6/7 Hrs of VPg

2007-01-29T11:57:00.000+06:00

6/7 hours (another 2/3 hrs in writing this entry) ... searching through net.... lots of research papers... At last, I've figured it out.

Yesterday, SRK was taking her lecture on plus strand RNA virus: Poliovirus and its life cycle.

The genome length of this novel (!!!) virus is 7500 b (According to SRK, but I think it varies. I've seen the range 7440 to 7700 b in different research papers.) Some features of Poliovirus genome are given below:

1. It has a covalently attached protein, VPg, at its 5' end. (¹)
2. Poly (A) tail at 3' end.
3. Three types of genes are present in this monocistronic genome: Structural, Protease (or proteinase) and RNA polymerase (from 5' to 3' respectively.) These genes are translated as single long polyprotein (~247 kD).

(right click and open in new window or tab to view enlarged image)

4. The proteinase has autosplicing capability. At first, it splices out itself, then it cleaves the polypeptide into different structural proteins and enzymes.

The list can be made much longer.

SRK said, poly (A) tail is required for infectivity, but VPg isn't. Later she said, RNA strand without covalently attached VPg can't be incorporated into viral capsid in maturation stage. I thought there was something missing... but I preferred not to ask. But this time Shammu was the person. She asked,"How can a RNA virus (or its RNA) be infective when it can't be inserted into viral capsid?" It was a good question, and I think I gave the answer in the class. But SRK didn't get my answer. Actually she didn't get the question either. She checked her lecture sheet and a book she brought with her (most probably Brock's Microbiology), then she dismissed one of her previous words. She thought it was her old book which is responsible. She told, "Forget about the sentence, "RNA with VPg can't be transcribed."...Well, Well, Well... this is another new statement. I don't think she told this before! May be I've missed.

So how to solve the puzzle. Remember none of her statements were wrong.

I've read some research papers published in different journals in between 1977 and 2006. The riddle is nearly solved ;)

VPg acts as a primer for new RNA strand synthesis (for both"+" and "-" strand synthesis.(^2,3)) It also stabilizes the RNA in cellular milieu. Recall cellular mRNAs are stabilized by 5'-cap. So VPg is necessary for replication of viral RNA. The RNA polymerase is coded by viral genome. RNA dependent RNA polymerase (RDR)... this enzyme requires primer, as far as I know other RNA polymerase don't require primer.

So what about translation? Before translation, VPg is cleaved by cellular enzymes. RNAs attached to VPg can't be translated. The reason isn't still known, but it is thought that VPg interferes with some steps in translation. (²) 3D folded structure, ~~Cis-acting Replication Element (cre) which along with~~ Internal Ribosome Entry Site (IRES) plays vital role in initiation of translation... ~~I am not sure whether cre and IRES are the same sequences or two different sequences... I'll update when I know.~~

Update: cre isn't necessary for translation, rather it is required for replication. cre is located within IRES but mutation in conserved cre region (AAACA motif) doesn't effect the rate of translation. (⁴)

Hurray! The dilemma is solved at last. Polio RNA without VPg is infectious since it can carry out penetration, translation, synthesize new VPg protein which can act as primer for new RNA synthesis by RDR. So infection continues... but this RNA can't be incorporated in Capsid in maturation phase! Who cares that? It is creating effective progeny, it is infecting its host, effectively stopping host translation... Fantastic Job! But the poor RNA itself dies with its host. An altruist.

Image Courtesy:
Poliovirus:
http://users.wfu.edu/banklm3/cell/index.html
Translation in Poliovirus:
http://pathmicro.med.sc.edu/book/virol-sta.htm

References:

1. Yuan Fon Lee et al., A Protein Covalently Linked to Poliovirus Genome RNA, 1977;74;59-63 PNAS oi:10.1073/pnas.74.1.59.

2. Akio Nomoto et al., The 5'-terminal Structures of Poliovirion RNA and Poliovirus mRNA Differ Only in the Genome-Linked Protein VPg, Proc. Natl. Acad. Sci. USA, Vol. 74, No. 12, pp. 5345-5349, December 1977.

3. Timothy J.R. Harris et al. Nucleic Acids Research, Vol. 8, No. 6, 1980.

4. Mason et al., Identificationand Characterizationofa cis-Acting Replication Element (cre) Adjacent to the Internal Ribosome Entry Site of Foot-and-Mouth Disease Virus, JOURNAL OF VIROLOGY, Oct. 2002, p. 9686–9694

12 hours and your cancer is cured!

2007-01-28T08:09:00.000+06:00

Sometimes life is really tough. This entry was supposed to be in last Monday or Tuesday...

It's BAS. (Baizid Alam Shibib)

Last Monday, he came to the class and started day dreaming ;)

He was asking,"If someone from Bangladesh invents a drug which cures any type of cancer within 12 hours, will s/he get Nobel Prize?" I said,"Not once..."

How can a biochemist have such fantasy? When I told Tanaeem, he laughed and said,"This joker has no idea. Complications like cancer; curing in 12 hour! It is not a disease. You can't go and kill the pathogens! It's your cells dividing uncontrollably and bringing back the control requires hack of a time!!! At least couple of months, in fact years."

He could have increased his credibility! He could have said any particular cancer, may be in a month or 6 months... that would have made lot sense. All cancer! He has no idea how cancer forms. There are at least millions of ways: activation of oncogene, inactivation of tumor suppressor genes... non-functional cell signaling... mutation ... I don't think the list will ever end. And if someone says, he wants to treat all these with one and only drug (when I can't even list them in single sentence), then I guess he has problem in grasping the difference between cancer and other diseases... funny thing is he teaches Human Physiology in Department of Biochemistry. To add to the surprise list, Biochemistry students think he is the moving encyclopedia!!! Ha Ha Ha!

May be he meant Astrology's Cancer ;)

The Job of A Teacher

2007-01-21T20:03:00.000+06:00

It was in DJ's class and I was bit confused about Physical Map of chromosome. Even though she didn't ask... it came up in my mind and I wanted to use this term. Yet I restrained. I had logics behind my idea. But I knew she wouldn't accept unless I'm right. Of course she is right in saying that I'm wrong. But not before hearing my explanations.

What's the job of a teacher? Is it just going to the class and deliver a pre-written speech like our President? I don't think so. Teaching is an interacting profession where your students are more important than you yourself. The most important part of teaching is developing your student's the quality of being critical to something, some ideas, concepts and developments. It's not like you go to your students, ask a question and reply, "Oh .... You are at the same place as yesterday."

I hate this rubbish educational system.

Image Courtesy: www.nature.com

A Brand New No and Puzzled SRK

2007-01-19T14:12:00.000+06:00

Today's Topic: SRK. (For those who don't know, SRK stands for Sanchita Rahnuma Khan.)

Yesterday she was taking class on Horizontal Gene transfer between bacterial species, especially Transduction. As an intro she mentioned Zinder & Lederberg experiment. She told, in the experiment observed frequency of gene transfer between two auxotrophs were 10^-5. Anyway, she continued with her lecture. In the class I came to know following facts:

Firstly, the frequency of DNA transfer from bacterial genome to phage genome is 1-2 %.

Secondly, the frequency of DNA transfer from phage to another bacteria is 1-2%.

Taking these facts together, my calculation was the frequency of gene transfer would be 10^-4. The 10X anomaly can be explained if we consider the fact that each DNA transfer might not result in complete Gene transfer. But she gave another brand new data!!! She said, the frequency of gene transfer by transduction is around 10^-6. This was completely unexpected. I was wondering to solve the mystery of 10^-4 and 10^-5, instead a new data of 10^-6 came up. I was completely puzzled and brought the facts into her notice. To be honest, I asked her out of curiosity, I didn't mean to harass her. (If you are a teacher, I think you would prefer not to have me in your class ;). Cause I can create lots of troubles when I want to, and sometimes I do.) Felt sorry looking at her face and I myself tried to cover up things by answering from my instincts. Anyway, she told us to check things out.

I've downloaded Zinder & Lederberg's paper, read couple of pages. The paper is kind of clumsy, but I think I'll be able to figure it out...

Lamark and AAA

2007-01-17T18:20:00.000+06:00

It's AAA today ;)

He was taking developmental biology. Nothing new, same old Triple A style. Suddenly I was stunned hearing some of his words!!! Was I hearing right? He said, memory is an important attribute in higher organism's cell... kind of Ok so far. Afterwards, as an example he said, experience from parents are passed to their offspring through cells. Gosh! Am I in 21st century? How can someone advocate Lamarkism which died in 19th century Darwinian Era? I should have argued with Akandh Sir. It's the old habit. I know there is no point. Critical thinking isn't appreciated in this failed educational system. Hail Memory! That's the only slogan here.

Another analogy which he wanted to draw appeared bit absurd to me. He said a shoe and an aeroplane manufacturing factory doesn't use the same material and technology. Likewise biologists expected distinct variation when they studied development of different multicellular organisms... but they were surprised to see the extent of similarity. Well, shoe and aeroplane are completely different things, their difference isn't even analogous to the difference between prokaryotes and eukaryotes. If he compared the production strategy of car and aeroplane, I think he would have found lots of similarities. The apparent similarity is at the same time a fascinating and a frustrating thing. Fascinating because it shows us the fundamental similarity, while it's frustrating because it testifies the fact that there are lots of to be discovered stuffs.

Meiosis: Who knows, me or DJ?

2007-01-16T18:45:00.000+06:00

Net connection is awesome today.

I thought there was no DJ today, became surprised to see it was in the routine.

Today she discussed sex determination, chromosome, chromatin fibre, mitosis and meiosis. A question came in my mind when DJ was delivering her lecture. Why X and Y chromosome's are named so? I googled net and found the answer from Google books.

Q: Why X & Y chromosomes are named so?

Ans: A common misconception about X and Y chromosome is that they are named because of their shape. However, Hermann Henking named the X because it was mysterious, or exceptional in some way and that Nettie Stevens then simply continued the alphabetical sequence when she named the Y.

(Source: The X in Sex: How the X Chromosome Controls Our Lives By David. Bainbridge)

When DJ started mitosis and meiosis, I got confused whether she knows those terms or not?

Life starts through meiosis, after fusion of egg and sperm!!! I don't get any of this, especially when she is saying about Homo sapiens. (Her words are correct for haploid organisms who undergo meiosis when diploid zygote is formed.) I've to wait and see.

(Right click and open in new window or tab to view enlarged image)

Another confusion arose when she asked, "What is the difference between Chromatin fibre and Chromosome?" Different answers came from different corners. I think some of them were right, though weren't complete. Chromatin fibre is non-condensed string of nucleosome which divides and condenses before cell division. This condensed form of chromatin fibre is known as chromosome. (Appears H shape in typical karyotype). Anyway, DJ rejected them. Instead she accepted Maruf's lead (partially) which I found the least appropriate.

She also talked about Genetic Maps. I know there are three types of maps, but right now, I can't recollect.

DJ Siamese!!!

2007-01-14T17:24:00.000+06:00

Toady DJ was taking class... she mentioned about Siamese Cat and related stuffs, the pigmentation pattern. One thing I found quite strange. She said, if we take a Siamese Cat to polar regions, it will turn into black completely! The logic was, since the temperature sensitive melanin producing enzyme (tyrosinase) will be functioning. I thought this was a rubbish idea.

Say we took a Siamese Cat to polar region (or incubated it in low temperature). If the mutant melanin producing enzyme had to function, the temperature of individual cells or tissues has to drop and more importantly the drop in temperature should sustain for a reasonable time (since melanin itself isn't mutant, rather one of melanin producing enzymes are mutant. You need time to synthesize melanin and make it express). This is quite unrealistic. In the extremities (or peripheral regions), the temperature is low. The reason being there is relatively low blood supply to exposed surface area ratio. High surface area is responsible for high heat loss rate, low blood supply amplifies the situation (Because blood is directly involved in temperature homeostasis). Theoretically in polar region, we may expect a Siamese Cat turn into completely black, but practically rapid temperature loss will lead to coma and eventually death long before you can see this bizarre hypothetical phenomenon.

Arguing with DJ has no point, those who know her personally will surely agree with me ;) .

Evolution, ID and Science

2007-01-11T00:34:00.000+06:00

Those who say Evolution is unscientific, they have difficulty in grasping the beauty of Evolution.

But those who say Intelligent Design is scientific, they don't understand science at all.

Ignorance Vs Truth

2006-12-19T18:07:00.000+06:00

I am shocked!!!! This is a victory of ignorance and bureaucracy over truth. I am amazed to see the naturte of allegation; 7 years back... I've enough doubt whether the development of genetic engineering was as advanced to engineer HIV virus!!!- That's what the lawers of the patients said. Funny logic indeed.

Initially Libya contacted Luc Montagnier, the co-discoverer of HIV virus, to conduct inspection of the mass outbreak of AIDS. Luc Montagnier's report cleared the Palesteinian Doctor and Bulgarian Nurses, instead he accused dirty condition of the Libyan Hospital (which is considered one of the best there). Libyan court rejected the report citing the report contradicted Libyan doctor's initial report. - What an idiotic reason behind rejecting!!!

There is still an option of appeal. Hope the court will uphold Justice....

Below goes the news from Yahooo News:

Libya sentences Bulgaria nurses to death

By KHALED EL-DEEB and WILLA THAYER, Associated Press Writers

TRIPOLI, Libya - Five Bulgarian nurses and a Palestinian doctor were convicted and sentenced to death by a Libyan court Tuesday on charges they deliberately infected hundreds of children with the
AIDS virus. The verdict can be appealed.

Judge Mahmoud Hawissa read out the verdict at a seven-minute hearing in a Tripoli court at the end of the defendants' second trial.

The six defendants, detained for nearly seven years, had previously been convicted and condemned to death, but Libyan judges granted them a retrial after international protests over the fairness of the proceedings. Bulgaria contends the children were infected by unsanitary practices at their Libyan hospital.

An international legal observer, Francois Cantier of Lawyers Without Borders, criticized the retrial as lacking scientific rigor. Research published this month said samples from the infected children showed their viruses were contracted before the six defendants started working at the hospital in question.

"We need scientific evidence. It is a medical issue, not only a judicial one," Cantier said after the verdict.

The long trial of the six foreign medical workers has become a bone of contention in Libyan leader Moammar Gadhafi's efforts to rebuild ties with the West. Europe and the United States have called for their release, indicating that future relations with Libya would be affected by Tuesday's verdict.

But Libyans strongly supported a conviction. Some 50 relatives of the infected children — about 50 of whom have already died of AIDS — waited outside the court early Tuesday morning, holding poster-sized pictures of their children and bearing placards that read "Death for the children killers" and "
HIV made in Bulgaria."

When the Supreme Court ordered a retrial in December 2005, friends and relatives rioted in Benghazi, the Libyan city where the children were infected in a state hospital.

Bulgarians will no doubt be disappointed by Tuesday's verdict. Hundreds of people staged peaceful protests in support of the five nurses in Bulgaria on Monday.

Europe, the United States and international rights groups have accused Libya of prosecuting the six foreign staff as scapegoats for dirty conditions at the Benghazi children's hospital.

Luc Montagnier — the French doctor who was a co-discoverer of HIV — testified in the first trial that the virus was active in the hospital before the Bulgarian nurses began their contracts there in 1998.

More evidence for that argument surfaced on Dec. 6 — too late to be submitted in court — when Nature magazine published an analysis of HIV and hepatitis virus samples from the children.

Using changes in the genetic information of HIV over time as a "molecular clock," the analysts concluded that the virus was contracted before the six defendants arrived at the hospital — perhaps even three years before.

Idriss Lagha, the president of a group representing the victims, rejected the Nature article, telling a news conference in London on Monday that the nurses had infected the children with a "genetically engineered" virus. He accused them as doing so for research on behalf of foreign intelligence agencies.

When the defendants were allowed to give evidence last month, they denied intentionally infecting children.

"No doctor or nurse would dare commit such a dreadful crime," said nurse Cristiana Valcheva, adding that she sympathized with the victims and their families.

A second Bulgarian, Valentina Siropulo, testified that of her seven years in Libya, "I've spent only 6 months working as a nurse and the rest of the time in prison."

Gadhafi, who has been trying to refashion his image from leader of a rogue state, got his government to ask Bulgaria to pay compensation to the children's families.

But Sofia rejected the idea as indicating an admission of the nurses' guilt.

Non-Vegeterian or Herbi-phobe!!!

2006-12-01T18:31:00.000+06:00

I don't know when it actually started. I had never liked plants. Not as food though.

During HSC I had left the plant part(classification and most part of plant physiology) nearly untouched. Still I managed to get A+ !!!

Still I don't like this altruistic (!!!) Eukaryote.

Those who have minimal knowledge of Life science surely know-plants are the organisms who capture sunlight, store them as chemical energy which is later used up by all the living organisms.

I was planning to write this post after reading the book Plant Physiology by Ross and Salisbury, most probably. (You can check whether I am right or not from my last post. It's the same book I'm trying to mention.) I was giving a bird's eye view over the book. Plant physiology has lots of interesting stuffs (like any other science). I came to know about the fact of plant ventilation, I've never imagined plants can be that complex... The true beauty of nature is it keeps you wondering all the time. Still I prefer other organisms over plants as a model organism for my research... They can be Prokaryote, Archaea and all Eukaryote except plants. We all have strange choices, don't we?

Well, then if you ask me, " How would you like to define plant?" That's a tricky question. Am I going to consider all photosynthetic organisms as plants? May be not. It's again mind's call ;)

My first preference is working with eukaryotes, especially multicellular ones. Cell differenciation and signalling, Developmental Biology, Oncology are my hot favourates. When I was in 1st year I wished to work in Immunology. Archaea is another special group that has always fascinated me.

Time will say what will happen.

NB:- Herbi-Phobe= Herb+Phobe (You'll not find this word in any dictionary, I've created myself ;))

Image Courtesy: Mark Harden's Archive

Actual Image link: http://www.artchive.com/artchive/m/mondrian/mondrian_red_tree.jpg

Missing Communication

2006-11-15T12:02:00.000+06:00

Last night, I was going through pages of Plant Physiology by Ross & Salisbury. I came up with a box entitled “Must We Write?” by Page W Morgan. The objective was why and how to write? It was in interesting comprehension in terms of both content and purpose.

It’s not surprising to me when I found the box stating that most of the science students find writing and communicating rather a useless time spending (which view I used to hold as well ;)). He put down some arguments against this. I think he was quite clear in his points.

I don’t like verbal communication with lots of people in general. But not sure what would be my attitude if the subject of communication is unknown to most of the listeners (Somehow I’ve the feeling that I will enjoy then.) But writing stuffs was never that irritating and boring to me.

Reading that article, I felt we miss one thing badly here in Bangladesh. It’s the lack of opportunities in developing communicating skills. There isn’t much we can do as students. In our department, DJ is trying to do something new. But I don’t like her approach. Anyway, everyone has his/her own style. We must learn to respect others. That’s one of the things we all have to learn.

Noble Achievement

2006-10-21T21:15:00.000+06:00

This year Nobel Peace Prize (2006) was awarded to a Bangladeshi person, Dr Muhammad Yunus and an organization, Grameen Bank. It is a remarkable thing for this poverty striken corrupted politician led country. I had no intention to post an entry on this subject. But some SMS's from friends and posts in groups prompted me to sit for this entry.... again got confused where to post (I've so many blogs ;)).

Some said, at last they (indicating to West) had to recognize us... some other thought after achieving this prize we can do anything... Blah Blah Blah.

Well, Nobel Prize isn't a recoginition of something... Someone didn't get Nobel Prize doesn't mean s/he didn't do good for Humanity. There is a selection board, there are lots of people and organizations to be considered. At the end, you select one or couple of them. That doesn't mean others did nothing.

Every nation has its talents, the matter is getting opportunity.

Another thing, very few Bangladeshi do great things. Our education system is such a numb one that it makes us shed all the humanly qualities, creativity, innovation. Besides unfortunately our society does neither respect nor reward the great peoples.

I don't know much about Bangladeshi born scientists who are doing good job abroad (I know only about my Shejho Mama, Dr Fazlul Huq who was once nominated for Nobel Prize for his Anti-cancer research), but it's for sure that no Bangladeshi working in Bangladesh is doing Nobel Prize winning science. There is no funding, besides you don't even get appreciation and inspiration for carrying out research.

May be someday things will change.

Image Courtesy: www.nobelprize.org

Expression and Interferance gets Nobel

2006-10-09T05:26:00.000+06:00

I'm kind of late with this post. I wanted to post when the prize of Medicine or Physiology was declared, but now Chemistry Nobel is already declared. So both at once.

Medicine or Physiology got Nobel on RNAi or RNA interferance. The work is itself simply groundbraking and marvellous. You know just after the publication, you deserve Nobel prize. Details of RNAi can be found in the following links

1. For General People.
2. Advanced Information.

It was a remarkable feat for Andrew Z. Fire & Craig C. Mello, recieving within ~ 7/8 years of reporting.

The Chemistry Prize went to Roger D Kornberg son of another Nobel Laurate Arthur D Kornberg. His work was on Eukaryote gene expression and its regulation. He coined the presence of Mediators in EK gene regulation. Details can be found in the following links

1. For General People.
2. Advanced Information.

Gene expression sweeps Nobel this year, whats next???

Claiming my Blog

2006-09-22T19:07:00.000+06:00

Technorati Profile

Folding or Misfolding???

2006-09-21T13:52:00.000+06:00

I's thinking about protein folding... there are terms like misfolding, unfolding and folding.

Misfolding is kind of misleading term. As far as I remember in Biochem texts Misfolding refers to 3D arrangements other than native conformation. Then what's the native conformation??? You'll asnwer the conformation that's found naturally... more or less that's the prevalent concept.

I've problem in accepting the word Naturally. I think each and every protein has millions of naturally occuring confoormations... even if the sequence of amino acids is identical (after all the melieu isn't identical) . What you're referring as Misfolding today might appear to be the most abundant fold... We don't have what's going through most of the life forms.

Instead of Misfolding we should use Variations of Folding Pattern.

Human mind is like proteins also. There are lots of ideas, concepts, thoughts... and most importantly they are environment dependent. The view you're holding today might be well differnt from the view of tomorrow's you.

That's enough for explaining the Title of my Newest Blog.