December 30, 2008

prep4md.com nominated as "Best Medical Weblog of 2008"

A couple of days ago I noticed that prep4md has been nominated for "Best Medical Weblog" of 2008 on medgadget.


Thanks for nominating me Brocasarea!


I nominated the following blogs:

---Best Medical Technologies/Informatics Weblog

Science Roll
http://scienceroll.com/


Indulge in the fascinating world of radiology and nuclear medicine
http://tomographyblog.com/


---Best Medical Weblog

Vitum Medicinus
http://blog.vitummedicinus.com/


Monash Medical Student
http://jeffreyleow.wordpress.com/


Half MD
http://halfmd.wordpress.com/


-------------------


You can nominate blogs here.
You can check the nominees here.


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December 27, 2008

What is "Mitochondrial Eve"?



As you may have already noticed I have been into evolution and that sort of readings in the past couple of weeks (as aparant from my book list).

I was just reading "River Out Of Eden"by Richard Dawkins and came across some amazing stuff that (as usual) I cannot resist sharing with you ;)

Let me quote straight from the book. At the end of one of the chapters he says:

"We may come to the following conclusions:

First, it is necessarily certain that there existed on female who we may call Mitochondrial Eve who is the most recent common ancestor of all modern humans down the female only pathway.

Second, It is also certain that there existed only one person of unknown sex who we may call the Focal Ancestor who is the most recent common ancestor of all modern humans down any pathway.

Third, although it is possible that the Mitochondrial Eve and the Focal Ancestor are one and the same it is vanishingly unlikely that this is so.

Forth, it is somewhat more likely that the Focal Ancestor was a male than a female.

Fifth, Mitochondrial Eve very probably lived less than a quarter of a million years ago.

Sixth, there is disagreenment where Mitochondrial Eve lived but the balance of informed opinion still favours Africa."


OK, if you do not have much previous knowledge in this field of science lets elaborate a little bit using (as usual) Wikipedia.



What or Who is the so-called Mitochondrial Eve?

Mitochondrial Eve a.k.a (mt-mrca) is the name given by researchers to the woman who is defined as the matrilineal most recent common ancestor (MRCA) for all currently living humans. Passed down from mother to offspring, her mitochondrial DNA (mtDNA) is now found in all living humans: every mtDNA in every living person is derived from hers.

Mitochondrial Eve is the female counterpart of Y-chromosomal Adam, the patrilineal most recent common ancestor, although they lived at different times.

She is believed to have lived about 140,000 years ago in what is now Ethiopia, Kenya or Tanzania. [citation needed] The time she lived is calculated based on the molecular clock technique of correlating elapsed time with observed genetic drift.

Mitochondrial Eve is the MRCA of all humans via the mitochondrial DNA pathway, not the unqualified MRCA of all humanity. All living humans can trace their ancestry back to the MRCA via at least one of their parents, but Mitochondrial Eve is defined via the maternal line.

Therefore, she necessarily lived at least as long, though likely much longer, ago than the MRCA of all humanity.


Please read this carefully cuz it may not be apparent at first:


The existence of Mitochondrial Eve and Y-chromosomal Adam does not imply the existence of population bottlenecks or a first couple. They each may have lived within a large human population at a different time.



What is Mitochondrial DNA?


Mitochondrial DNA (mtDNA) is the DNA located in organelles called mitochondria. Most other DNA present in eukaryotic organisms is found in the cell nucleus.

Stress on this part: Nuclear and mitochondrial DNA are thought to be of separate evolutionary origin, with the mtDNA being derived from the circular genomes of the bacteria that were engulfed by the early ancestors of today's eukaryotic cells. I bet you did not know that!!! Did you???

Each mitochondrion is estimated to contain 2-10 mtDNA copies. In the cells of extant organisms, the vast majority of the proteins present in the mitochondria (numbering approximately 1500 different types in mammals) are coded for by nuclear DNA, but the genes for some of them, if not most, are thought to have originally been of bacterial origin, having since been transferred to the eukaryotic nucleus during evolution.


If you studied molecular biology you should already know this:


In most multicellular organisms, mtDNA is inherited from the mother (maternally inherited).


What amased me was the the mechanism of this:


Mechanisms for this include simple dilution (an egg contains 100,000 to 1,000,000 mtDNA molecules, whereas a sperm contains only 100 to 1000), degradation of sperm mtDNA in the fertilized egg, and, at least in a few organisms, failure of sperm mtDNA to enter the egg.

Whatever the mechanism, this single parent (uniparental) pattern of mtDNA inheritance is found in most animals, most plants and in fungi as well.

Mutations in mtDNA can in some cases cause maternally inherited diseases and some evidence suggests that they might be major contributors to the aging process and age-associated pathologies. [citation needed] In humans (and probably in metazoans in general), 100-10,000 separate copies of mtDNA are usually present per cell (egg and sperm cells are exceptions). In mammals, each circular mtDNA molecule consists of 15,000-17,000 base pairs, which encode the same 37 genes: 13 for proteins (polypeptides), 22 for transfer RNA (tRNA) and one each for the small and large subunits of ribosomal RNA (rRNA).



Some misconceptions:


Mitochondrial Eve is the most recent common matrilineal ancestor, not the MRCA of all humans. The MRCA's offspring have led to all living humans via sons and daughters, but Mitochondrial Eve must be traced only through female lineages, so she is estimated to have lived much longer ago than the MRCA. According to probabilistic studies, Mitochondrial Eve is thought to have lived around 140,000 years ago.



I believe this is an important point to make:

Allan Wilson's naming Mitochondrial Eve after Eve of the Genesis creation story has led to some misunderstandings among the general public. A common misconception is that Mitochondrial Eve was the only living human female of her time. Had this been the case, humanity would have long since become extinct due to an extreme example of a population bottleneck. Indeed, not only were many women alive at the same time as Mitochondrial Eve but many of them have living descendants through their sons. While the mtDNA of these women are not as common as the MRCA, their Nuclear genes are present in today's population.

------------------------------



Did you know all of this? Are you interested in such topics? Please leave a comment :-)



Photo credit: Canadacow - Creative Commons


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December 25, 2008

An appeal from Wikipedia founder, Jimmy Wales

An appeal from Wikipedia founder, Jimmy Wales


"Dear Reader,

Today I am going to ask you to support Wikipedia with a donation. This might sound unusual: Why does one of the world's five most popular web properties ask for financial support from its users?

Wikipedia is built differently from almost every other top 50 website. We have a small number of paid staff, just twenty-three. Wikipedia content is free to use by anyone for any purpose. Our annual expenses are less than six million dollars. Wikipedia is run by the non-profit Wikimedia Foundation, which I founded in 2003.

At its core, Wikipedia is driven by a global community of more than 150,000 volunteers - all dedicated to sharing knowledge freely. Over almost eight years, these volunteers have contributed more than 11 million articles in 265 languages. More than 275 million people come to our website every month to access information, free of charge and free of advertising.

But Wikipedia is more than a website. We share a common cause: Imagine a world in which every single person on the planet is given free access to the sum of all human knowledge. That's our commitment.

Your donation helps us in several ways. Most importantly, you will help us cover the increasing cost of managing global traffic to one of the most popular websites on the Internet. Funds also help us improve the software that runs Wikipedia -- making it easier to search, easier to read, and easier to write for. We are committed to growing the free knowledge movement world-wide, by recruiting new volunteers, and building strategic partnerships with institutions of culture and learning.

Wikipedia is different. It's the largest encyclopedia in history, written by volunteers. Like a national park or a school, we don't believe advertising should have a place in Wikipedia. We want to keep it free and strong, but we need the support of thousands of people like you.

I invite you to join us: Your donation will help keep Wikipedia free for the whole world.

Thank you,

Jimmy Wales"



To donate Click Here


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Evolution 101 for dummies

Note: Please before talking or trying to debate something learn, read, research, and educate your self about the topic otherwise believe me you will sound like this:



OK, lets try and scratch the surface together, so we do not sound like idiots too.


What is evolution?

In biology, evolution is change in the inherited traits of a population of organisms from one generation to the next. These changes are caused by a combination of three main processes: variation, reproduction, and selection. Genes that are passed on to an organism's offspring produce the inherited traits that are the basis of evolution. These traits vary within populations, with organisms showing heritable differences in their traits. When organisms reproduce, their offspring may have new or altered traits. These new traits arise in two main ways: either from mutations in genes, or from the transfer of genes between populations and between species. In species that reproduce sexually, new combinations of genes are also produced by genetic recombination, which can increase variation between organisms. Evolution occurs when these heritable differences become more common or rare in a population.

Two major mechanisms drive evolution. The first is natural selection, a process causing heritable traits that are helpful for survival and reproduction to become more common in a population, and harmful traits to become more rare. This occurs because individuals with advantageous traits are more likely to reproduce, so that more individuals in the next generation inherit these traits. Over many generations, adaptations occur through a combination of successive, small, random changes in traits, and natural selection of those variants best-suited for their environment. The second major mechanism is genetic drift, an independent process that produces random changes in the frequency of traits in a population. Genetic drift results from the role probability plays in whether a given trait will be passed on as individuals survive and reproduce. Though the changes produced in any one generation by drift and selection are small, differences accumulate with each subsequent generation and can, over time, cause substantial changes in the organisms. This process can culminate in the emergence of new species. Indeed, the similarities between organisms suggest that all known species are descended from a common ancestor (or ancestral gene pool) through this process of gradual divergence.

Evolutionary biology documents the fact that evolution occurs, and also develops and tests theories that explain its causes. Studies of the fossil record and the diversity of living organisms had convinced most scientists by the mid-nineteenth century that species changed over time. However, the mechanism driving these changes remained unclear until the 1859 publication of Charles Darwin's On the Origin of Species, detailing the theory of evolution by natural selection.

Darwin's work soon led to overwhelming acceptance of evolution within the scientific community.

In the 1930s, Darwinian natural selection was combined with Mendelian inheritance to form the modern evolutionary synthesis, in which the connection between the units of evolution (genes) and the mechanism of evolution (natural selection) was made.

This powerful explanatory and predictive theory directs research by constantly raising new questions, and it has become the central organizing principle of modern biology, providing a unifying explanation for the diversity of life on Earth.


------------------------------------------------

Here are some FAQ:


Isn't evolution just a theory that remains unproven?

In science, a theory is a rigorously tested statement of general principles that explains observable and recorded aspects of the world. A scientific theory therefore describes a higher level of understanding that ties "facts" together. A scientific theory stands until proven wrong -- it is never proven correct. (do we have that clear now!!!!!) The Darwinian theory of evolution has withstood the test of time and thousands of scientific experiments; nothing has disproved it since Darwin first proposed it more than 150 years ago. Indeed, many scientific advances, in a range of scientific disciplines including physics, geology, chemistry, and molecular biology, have supported, refined, and expanded evolutionary theory far beyond anything Darwin could have imagined.


Is there evidence for evolution?

In the 150 years since Darwin proposed the theory of evolution by natural selection, a mountain of evidence has accumulated to support the theory. A greatly expanded fossil record since Darwin's time, the discovery of DNA and the process of genetic replication, an understanding of radioactive decay, observations of natural selection in the wild and in laboratories, and evidence in the genomes of many different organisms, including humans, have all bolstered the validity of the theory of evolution.

Did we evolve from monkeys?

Humans did not evolve from monkeys. Humans are more closely related to modern apes than to monkeys, but we didn't evolve from apes, either. Humans share a common ancestor with modern African apes, like gorillas and chimpanzees. Scientists believe this common ancestor existed 5 to 8 million years ago. Shortly thereafter, the species diverged into two separate lineages. One of these lineages ultimately evolved into gorillas and chimps, and the other evolved into early human ancestors called hominids. (in religion they preach that Adam and Eve descended from heaven, so what happens now?! I will leave this part for you to explain)

How does natural selection work?

In the process of natural selection, individuals in a population who are well-adapted to a particular set of environmental conditions have an advantage over those who are not so well adapted. The advantage comes in the form of survival and reproductive success. For example, those individuals who are better able to find and use a food resource will, on average, live longer and produce more offspring than those who are less successful at finding food. Inherited traits that increase individuals' fitness are then passed to their offspring, thus giving the offspring the same advantages.
-----------------------------------------------


Here is a collection of 24 videos from YouTube supporting the Theory of Evolution

#1
Listen to the scientists



Links to the other 23 videos in this series:
2: http://www.youtube.com/watch?v=g7Ctl9...
3: http://www.youtube.com/watch?v=jVaCmA...
4: http://www.youtube.com/watch?v=P6_Ktv...
5: http://www.youtube.com/watch?v=TNxXlq...
6: http://www.youtube.com/watch?v=9X50lH...
7: http://www.youtube.com/watch?v=JIzaeI...
8: http://www.youtube.com/watch?v=1BJa7W...
9: http://www.youtube.com/watch?v=3CCapu...
10: http://www.youtube.com/watch?v=mp7b9E...
11: http://www.youtube.com/watch?v=LzTlZo...
12: http://www.youtube.com/watch?v=SjXYZd...
13: http://www.youtube.com/watch?v=ske9pw...
14: http://www.youtube.com/watch?v=FxnJ8y...
15: http://www.youtube.com/watch?v=TkcC8F...
16: http://www.youtube.com/watch?v=7XDn5S...
17: http://www.youtube.com/watch?v=9KD3XY...
18: http://www.youtube.com/watch?v=1ZLOqJ...
19: http://www.youtube.com/watch?v=PVz6se...
20: http://www.youtube.com/watch?v=h2BVfP...
21: http://www.youtube.com/watch?v=q5PNzx...
22: http://www.youtube.com/watch?v=WrlYz0...
23: http://www.youtube.com/watch?v=KQbv6E...



---------------------
Resources:
Evolution --- Wikipedia
Common descent --- Wikipedia
Fitness (biology) --- Wikipedia
Natural selection --- Wikipedia
Introduction to evolution --- Wikipedia
Charles Darwin --- Wikipedia
Understanding evolution --- Berkeley
Some videos on the same topic from PBS
For more FAQ about evolution CLICK HERE. --- PBS

----------------------
Suggested books to read:

"The Selfish Gene" is a book on evolution by Richard Dawkins, published in 1976. It builds upon the principal theory of George C. Williams's first book Adaptation and Natural Selection. Dawkins coined the term selfish gene as a way of expressing the gene-centred view of evolution, which holds that evolution is best viewed as acting on genes and that selection at the level of organisms or populations almost never overrides selection based on genes.


Charles Darwin's "On the Origin of Species" (published 24 November 1859) is a seminal work in scientific literature and a landmark work in evolutionary biology. The book's full title is On the Origin of Species by Means of Natural Selection, or the Preservation of Favored Races in the Struggle for Life, while for the 6th edition of 1872 the title was changed to The Origin of Species. It introduced the theory that populations evolve over the course of generations through a process of natural selection. Darwin's book was the culmination of evidence he had accumulated on the voyage of the Beagle in the 1830s and expanded through continuing investigations and experiments after his return.

The book is readable even for the non-specialist and attracted widespread interest on publication. The book was controversial because it contradicted religious beliefs that underlay the then current theories of biology, and it generated much discussion on scientific, philosophical, and religious grounds.


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December 23, 2008

My Favorite Medical Basic Science Books

Note: This is not a USMLE Step 1 review book list and these are not necessarily the best books on the market. They are books that are dear to my heart. Either because they are the most that I have learned from or they were outstandingly well written and put together. I have read 10s of other basic science books but I think I will remember these longer down the road.

IMG_1052


IMG_1050


I have already published my USMLE Step 1 reviews books list and I published a list of links to the most helpful USMLE Step 1 exam experiences of those who scored 99.


What are your favorite basic science books?


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December 16, 2008

Notable books I have read


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Books I want to read

  • One Hundred Years of Solitude
  • Stop Me If You've Heard This One Before ... by David Yoo
  • Memoirs of a Geisha
  • The Pillars of the Earth ... by Ken Follett
  • The Prophet (Wordsworth Classics of World Literature) ... by Kahlil Gibran
  • Left To Tell: Discovering God Amidst the Rwandan Holocaust ... by Immaculee Ilibagiza
  • The Revolution: A Manifesto ... by Ron Paul
  • The Host: A Novel ... by Stephenie Meyer
  • It (Signet Books)
  • The Stand ... by Stephen King
  • Paper Towns


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Books I am Reading

  • Every Patient Tells a Story by Lisa Sanders
  • How Doctors Think by Jerome E. Groopman
  • The Time traveler's Wife by Audrey Niffenegger
  • Duma Key by Stephen King
  • The Universe in A Nutshell by Stephen Hawking
  • The Post American World by Fareed Zakaria
  • The God Delusion by Richard Dawkins
  • The World Without Us by Alan Weisman
  • Letter To A Christian Nation by Sam Harris
  • The Spiral Staircase by Karen Armstrong
  • The Greatest Show on Earth by Richard Dawkins

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Books

I have been planning on writing about this for quite a long time. Before I do, I am going to share some videos with you that I found randomly on YouTube which I hope will help me make my point in the up coming posts.


Dimensiontornfree's favorite books



Graphicsguy948's favorite books


voltopian's favorite books from last year


imaginaryjenn89's to read list for 2007


Thisisace read 50 books in one year


itsnotproper is trying to read 50 books this year


Laae10 is planning on reading 50 books this year too


McCain's and Obama's Favorite Books





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One of my new favorite blogs

IMG_0759



One of my favorite blogs these days that I have stumbled upon coincidently a couple of months ago is "The Big Picture" blog.

"The Big Picture is a photo blog for the Boston Globe/boston.com, entries are posted every Monday, Wednesday and Friday by Alan Taylor. Inspired by publications like Life Magazine (of old), National Geographic, and online experiences like MSNBC.com's Picture Stories galleries and Brian Storm'sMediaStorm, The Big Picture is intended to highlight high-quality, amazing imagery - with a focus on current events, lesser-known stories and, well, just about anything that comes across the wire that looks really interesting."

Some of the most significant posts that I read there were:



What is your favorite blog?


Image credit: prep4md - flickr

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December 15, 2008

Books on my non-medical wanna read list

IMG_0757


What is the best thing for you to do during the holidays? Read non medical books. Preferably novels. Especially those bulky 600 (or more) page novels. And make sure that you have 2-3 back ups in case you got tired from the one you are reading and so you can start the second one as soon as you finish the first one.

Whats the point? Filling up your spare time, personal enjoyment, and most importantly avoiding real human beings as much as possible. I assume you have been living long enough to notice that all problems arise from human contact and that is exactly what you do not want happening during your precious free time.

Thats why last summer I read like 10 non medical books (I will share those later on). And I think it is a good idea to repeat this strategy this holiday.


OK I'll cut the crap now, here is a list of books that I would like to read in the near future:

  • One Hundred Years of Solitude ... by Gabriel Garcia Marquez
  • Stop Me If You've Heard This One Before ... by David Yoo
  • Memoirs of a Geisha: A Novel ... by Arthur Golden
  • The Pillars of the Earth ... by Ken Follett
  • The Prophet (Wordsworth Classics of World Literature) ... by Kahlil Gibran
  • Left To Tell: Discovering God Amidst the Rwandan Holocaust ... by Immaculee Ilibagiza
  • The Revolution: A Manifesto ... by Ron Paul
  • The Host: A Novel ... by Stephenie Meyer
  • It ... by Stephen King
  • The Stand ... by Stephen King

Did you read any of the books on this list? Do you recommend any of them? Do you not recommend any of them? What types of non medical books do you like to read?


Photo credit: prep4md on flickr

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Will Facebook buy Twitter? + videos

"About three weeks ago, Facebook and Twitter ended several weeks of serious talks, in which Facebook was offering to acquire Twitter for $500 million of its stock, which also included a cash component.

While rumors of Facebook’s interest were brought up in an interview with Facebook CEO Mark Zuckerberg at the Web 2.0 Summit a few weeks ago ..." Read full article


Facebook parody:



Twitter parody:




Do you use either site?


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December 11, 2008

My new photography blog "SD1100IS"

The Great Nile


I launched a blog to host my photographs that I have been taking with my new Canon camera. You can check it out here: "SD1100IS"



Are you into photography? Where can we have a look at your photos?


Photo credit: prep4md

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What Image Opened Your Eyes to Human Rights? -video-



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Top 10 topics college students discuss over here

Top 10 things college students talk about over here.




  • Girls
  • Struggling with English as a second language
  • Losing faith and becoming less religious
  • Financial struggles and how they do not have enough money towards the end of the month
  • Things they do not like about attending school here
  • How they did really bad on their exams and how their professors screwed them
  • Restaurants that serve good and cheap food
  • TV shows
  • Marriage
  • Opening small businesses and making money on the side

What are the most common topics male students discuss where you are?



Photo credit: Dano - Creative commons.

December 10, 2008

My top 10 favorite NEJM "Image of The Week"

  • Ascariasis
  • Gravid Uterus in Hernia
  • Recurrent aspiration pneumonia
  • Two hearts
  • Meningioma
  • Cerebral embolism of probably aortic origin
  • Squamous cell carcinoma manifesting as a cutaneous horn
  • Ocular myiasis
  • Central pontine myelinolysis
  • Colonic saccular diverticula


All images are courtesy of NEJM.

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December 08, 2008

Where else can you find prep4md?

Here are some places you can find me other than here ...


Flickr:
http://flickr.com/photos/prep4md/

Twitter:
http://twitter.com/prep4md

Technorati:
http://technorati.com/people/technorati/prep4md

YouTube:
http://www.youtube.com/user/prep4md

FriendFeed:
http://friendfeed.com/prep4md


Of course there is Facebook, Amazon, SDN, and Prep4USMLE too!


What other sites do you think I should join?


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Web Illiterates WTF!

Berci Mesko from Scienceroll has been preaching web 2.0 and med 2.0 for at least two years now. I have noticed sometimes in the comments section of his blog people telling him stuff like: "who still doesn't know this?!" "Don't you think its too late to talk about this? everyone knows this by now" "why are you talking about web 2.0 this much? doesn't everyone know this?"


Well, to my astonishment, yesterday I was talking to two 2nd year medical students that I know. We where talking tech and discussing some websites. Along the conversation I mentioned Wikipedia as a good example of how collaboration online can be so effective and can help people around the world. The thing that struck me was that one of them had no idea what I was talking about. He had the "daaah"expressions on his face. Just to make sure, I asked him: "You know Wikipedia, right?"And he said: "NO". I asked him: "You never checked up something on there before?". And he said: "NO. I never heard of it."


I tried not to show him my astonishment fearing that I'll embarrass him and explained that it was simply an electronic encyclopedia that people form around the world contribute to. But seriously, WTF!


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I got me a Pro account on Flickr

I have been using my current laptop for two years and a half. Knowing how unreliable these PCs can be I am starting to back up my documents, files, videos, E-books, and audios. It has took me a long time to collect all of this stuff and I wouldn't like to lose it all in a blink just because of some stupid glitch or an electronic-nervous-breakdown!

Because of that and because I bought a new digital camera a couple of days ago I wanted to have somewhere safe to store my photos. And where else would I do that other than Flickr (one of my favorite sites!)? So tonight I upgraded my account to a "Pro" account. Now I have "unlimited" storage capacity. By the way, free accounts can only hold 200 pictures, which I exceeded a long time ago!

Here are some of the features you get with the Pro account:

  • Unlimited uploads and storage (as I said you can only store 200 photos with a free account - then they start hiding old photos and replace them with new ones. Notice I said they Hide the old ones and they do not Delete them)
  • Unlimited sets and collections (with a free account you can only have one or two sets)
  • Accsess to your original files (your photos that have been hidden previously because of exhausting your free account will reappear - is this brilliant marketing or what? lol)
  • Stats on your account (this is a nice feature, me thinks)
  • Ad-free browsing and sharing (it better be Ad-free , I paid 24 bucks for this!)
  • You can upload videos too (I didn't try this one yet, but from my experience with photos on the site I think it would work beautifully)
  • You can adjust the layout of your "photostream"
  • You can choose a custom domain for your profile and photo stream pages. Mine is: http://www.flickr.com/photos/prep4md/


I know that Kendra from Island Med Student and dokidok from USMLEMD already have accounts on flickr. I would like to know who else has an account over there.

Have a nice day guys :)


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