The Beginning of the End

Posted by :David Manly On : February 8, 2011
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Category: "The Black", Epic Writing Adventure, GeneGeek, The EWA, Twitter

With The Definitive Answers going strong, this seems like the perfect time to pile on even more onto my plate (but I couldn’t be more excited!)

As long-time readers know, I began writing a novel in the summer of 2009 entitled, “The Black.” It all started with a few sentences I wrote down at my job, that blossomed into a chapter that quickly became a whole synopsis of a novel. And so, I began to write.

On the right side of my blog, you will see the first five chapters of The Black, which people have shown genuine interest in me finishing. However, when school started once again that fall, it went on the back burner. It was never forgotten, just often swept-aside in favour of other projects.

But, that time has ended.

In collaboration with a friend on Twitter (@genegeek), this is the start of what we are calling, “The Epic Writing Adventure.”

The rules are simple:
1) Write a novel that totals at least 30,000 words (or write your thesis – just set a goal)
2) We have exactly one month to do it (February 16th – March 16th)
3) To monitor our progress, follow me (@davidmanly) and @genegeekon Twitter, or simply search #TheEWA hash-tag on Twitter
4) After the month, we will edit the novels and perhaps even look into ways to publish
5) ANYONE is welcome to join in on the writing adventure!
6) This adventure is open to both fiction and non-fiction, or even any type of long-form journalism or thesis.

If we get enough people involved with this, we will design a badge for your blog or wall so you can marvel at your great accomplishment once we’re done!

And simply because you have read the first few parts of my novel that I have put on my blog, doesn’t mean you know how the story begins. What I wrote before was simply a rough draft to keep me writing … you haven’t seen anything yet.

Things will be changed, edited, moved around, but the core story will stay the same:

“The Black” tells a story of a young lab assistant, who after a lab accident begins to view his past in flashes, starting from the moment of the accident to when he was born. But, the thing is, memories do not stop surfacing. Memories from before he was even born …”

Stay tuned for more!

The Definitive Answers

Posted by :David Manly On : February 3, 2011
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Category: AskDavidQuestions, The Definitive Answers

This marks the official beginning of my question experiment which I have decided to call, “The Definitive Answers.” You like it?

Are you ready? Let’s get started!

Out of all the questions I have received at askdavidquestions@gmail.com, I chose three for the official first post. If I did not select your question, do not worry, as I will get to them all soon!

Thank you all for your questions, keep them coming and help me spread the word!

Enjoy 🙂

It’s A Brand New Day

Posted by :David Manly On : January 26, 2011
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Category: Uncategorized

It’s a brand new day of a brand new year with a (somewhat) brand new blog!

But before I get to the reveal of The definitive host 3.0 upgrade, I have some other news to share first.

I have another post up on the Scientific American Guest Blog, this time about some of my favourite animals – Snakes!
The post is entitled, “Biting the hand that feeds: The evolution of snake venom.” I had an absolute blast writing it, and I hope you will all enjoy reading it.

Now, on to the main event. But instead of you reading what is coming up with my blog, let me tell you.

That’s right, this blog will now have a significant amount of time spent answering YOUR science questions that you have always wondered about but never quite understood. Is there anything you or anyone who know has always wondered about?

So go ahead, ask away!

I will try to answer each and every question I get, and if I cannot, I will find someone who can. But, for this to succeed, I need your help. Promote this blog, get people involved, and I think this could turn into something really, really special (but only if you help).

Please submit questions to: askdavidquestions@gmail.com

Thank you, and stay tuned!

A New Year, A New Start and New Possibilities

Posted by :David Manly On : January 5, 2011
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Category: 2011, Black footed ferrets, MRP, Scientific American

Happy 2011 everyone!

It is five days into the new year, and I hope everyone is still sticking to their New Year’s resolutions (or at least trying to).

I am excited and thrilled to say that the new year has started off with a bang, as something I wrote was chosen to be out on the Scientific American Guest Blog.

Yes, one of the most prestigious science magazines asked me to write a post, and I said yes without hesitation. But, now I was faced with the daunting task of what to write about.

Those of you who read my blog regularly know that in the summer of 2009, I embarked on a journey to South Dakota for my Masters of Journalism project to find an endangered species. My adventures were a very interesting one, and I always thought that there was more than enough material for my project as well as another article.

I pitched it to SciAm, and they loved it!

So, here is a more in-depth look at me spending a few days with “The Ferret Hunters”

Twelve Months of Manly

Posted by :David Manly On : December 15, 2010
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Category: Uncategorized

I have decided to do something which I have yet to do here on my blog, and that is participate in an Internet fad, which in this case is called “Twelve Months.”

The rules are simple:
-Post the link and first sentence from the first blog entry for each month of the past year.

So, let’s see what turns up!

January:
Two interesting things have happened to me over the past few days. (I had just gotten a letter in the mail from the Prime Minister’s Office)

February:
Yeah, I know it’s been a while. Yeah, I know you all have been eagerly awaiting my next post. (Posted all my tweets about the science conference I went to)

March:

Based on my background, as well as my thesis, many people assume that I am an animal guy through and through. Granted, my thesis was on frog salinity tolerance, and I know quote a bit about a vast majority of animals – but that is not my only area of interest. (Book review of SUPERBUG)

April:
NO Posts (Had just graduated and began looking for work in earnest)

May:
Welcome, welcome, welcome! (Changed the name of my blog to “The definitive host” from “Musings of a Manly.”)

June:
Sorry for the long delay between posts, but it’s gotten surprisingly hectic over here. (Posted my Masters project on black-footed ferrets)

July:
NO Posts (Working for someone in Texas)

August:
NO Posts (Went to Europe)

September:
NO Posts (Started a new full-time job, and did not make me want to write even more)

October:
Hey there folks, sorry for my prolonged absence! (Posted all the links to my LabSpaces posts that I had been making over the past few months)

November:
NO Posts (Sorry … but the job was eating up a lot of time)

December:
Are there aliens among us? (About the Arsenic Aliens story)

Quite the busy year, eh?

But don’t you worry, as this trend of months going by without a post shall continue no more!
One of my New Year’s Resolutions is to write more on my blog, as well as workout more and finish my novel … it’s going to be a great year 🙂

Aliens and Arsenic: A Love Story

Posted by :David Manly On : December 4, 2010
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Category: Alien Life, Aliens, Arsenic, Phosphate, Science, Scientific Discovery

NOTE: THIS POST IS TAKEN FROM MY NEWEST LABSPACES POST WHICH CAN BE FOUND HERE

Are there aliens among us?

Short answer – No, at least not yet.

Despite the journalistic frenzy that was the NASA press conference held a few days ago, the paper published in the journal Science about a rather unique organism that was hailed as “extraterrestrial” by the news media fell short of its promise.

Sadly, the organism they discuss is clearly terrestrial, albeit an odd one.

In the paper, the author’s discuss a bacterium that was able to use the element arsenic instead of phosphorus, but I’m getting ahead of myself. First, a little information is needed regarding DNA.

DNA possesses a backbone of a phosphate bound to a sugar molecule. The phosphate is a phosphorous atom bound to four oxygen atoms. Now remember this, it is important.

Arsenic, which is directly below phosphorus on the periodic table, shares many of the same properties with phosphorous. In fact, arsenic can bind with four oxygen atoms to create arsenate, which behaves in a very similar way to phosphate.

Now, what the researchers did in the science paper was go to Mono Lake in California and find an “extremophile” bacteria, which is a bacteria that can survive in extremely harsh conditions (such as very high salt, temperature, high concentrations of acid, etc…). The scientists then isolated a strain of the bacteria in the lab and began to examine it.

In the lab, the researchers fed the bacteria essential nutrients, including phosphate, with little arsenic. Then, they gradually removed phosphate and replaced it with increasing concentrations of arsenic.
Over time, there was no phosphate left in the nutrients and only arsenic. By probing the DNA and proteins of the bacteria, they found that the organisms were using arsenate instead of phosphate.

Basically, they had created arsenic-based life. They did not find arsenic-based life, but had experimentally created it.
 
This is where the news media got it wrong.

It’s just like my mom when she got me to eat spinach. She would place a few leaves of spinach into a salad, saying it was a different type of lettuce, and I would eat it all together and not be able to tell the difference. Gradually, the salads became more and more spinach and less lettuce, until there was no lettuce left.

When asked if I liked the ‘salad’ and I replied with a big yes, did my mother admit that there was no lettuce in the salad – just spinach. From then on, I began to eat spinach.

See, the bacteria uses phosphate just like us. They prefer it!

But, they are adapted to live in Mono Lake, which has high concentrations of arsenic (the ability to survive there is amazing in and of itself), and can incorporate it into their biological mechanisms when absolutely necessary.

Also, by taking a look at a diagram from the paper below, you can see that all was not well with the arsenate bacteria. In fact, the arsenic bacteria (D) took longer to grow than their phosphate counterparts (C), despite their increased size.

As well, the arsenic-reared bacteria had huge vacuoles (fluid filled sacs) within them. What those sacs mean is up to interpretation, as arsenic-based compounds are not very durable in water. Perhaps it was to segregate water from the fragile compounds?

Suffice to say, the discovery was cool, but it is not extraterrestrial life. It was alien, but not unlike a genetically altered E. coli or Drosophila.

Other questions also rise up regarding a phosphate-free existence:
–       What about ATP/ADP/AMP?
–       Were there traces amounts of phosphorous used in such low amounts that they were undetectable?
–       What about all other DNA replication, translation and transcription?

This research is interesting, and has some great potential, but is lightyears away from proof of extraterrestrial life.

Here is the paper from Science:
Wolfe-Simon, F., Blum, J., Kulp, T., Gordon, G., Hoeft, S., Pett-Ridge, J., Stolz, J., Webb, S., Weber, P., Davies, P., Anbar, A., & Oremland, R. (2010). A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus Science DOI: 10.1126/science.1197258

Also, here is a great article written by Carl Zimmer about the discovery, where he actually interviewed the lead author and researcher in the paper:
http://blogs.discovermagazine.com/loom/

What I’ve Been Up To Lately …

Posted by :David Manly On : October 19, 2010
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Category: Blog Posts, LabSpaces, The Wonderful World of Animals

Hey there folks, sorry for my prolonged absence!

I assure you, I have been extremely busy with juggling my four jobs, and as you can probably guess, they keep me pretty darn busy. So, I have decided to do something about it.

From now on, whenever I make a post on another website, I will link to it here. That way, everyone can see just how hard I’ve been working.

So, here are the link to all my latest posts for LabSpaces, starting with my very first one on the effects of the Gulf oil spill entitled, “The Effects of Oil on Wildlife.”

My next post was about the unique research currently being undertaken with snakes, called “It’s What’s on the Inside that Counts.”

Following that, there was a lot of news about the World Cup of Soccer. So, I decided to take a very interesting look at a rather unique animal involved in the World Cup – An octopus named Paul in “Ink-credible Invertebrates.”

Then, dabbling into a field in which I have enormous interest (infectious diseases), I decided to write a post about a rather unique way scientists are fighting malaria. The post was entitled “All the Bite, Without the Risk.”

After being asked by numerous people that read my blog on LabSpaces, I then decided to tell them all just “A Little Bit About Me.”

Before I went on my trip to UK and Europe (which was AMAZING), I was fortunate enough to be able to watch the greatest tv of the year – Discovery Channel’s Shark Week. Inspired, I wrote about what I believe to be “The Best Week of the Year.”

Upon returning the Canada, there was one story about my trip that I felt like I must share with those who read my LabSpaces blog. It happened to me in London, in a very old Abbey, called Westminster. Read all about what happened to me in “An Unexpected Surprise in London.”

In my continuing quest to try something new, I decided to use my brand new iMac and put up a video review of a book that the author had sent to me. Check out “My First Ever Video Book Review!”

Every month from now on, LabSpaces creates unique questions for the bloggers to answer. The one for this month was “what you would do if you weren’t doing what you’re doing now?” So, read the rather interesting answer of mine in “What I’d be doing if I wasn’t doing science – A Musical.”

Lastly, my most recent post was about how horses have adapted to run, and why when they fall, it is often an injury that they cannot recover from (the post was inspired by seeing the movie “Secretariat,” starring Diane Lane and John Malkovich).
My newest post is called “Off to the Races!”

Whenever I write a new post, I will post the link here for all to see.

Until then, you stay classy!

My Absence Explained!

Posted by :David Manly On : June 29, 2010
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Category: Geek Girls Network, Lab Spaces, lost, Nerdbastards, Twitter

I am sorry I have been away these past few weeks, but I assure you, I have a very good reason!

The week before my Master’s of Journalism graduation, I got offered a few opportunities to keep me busy. And since then, I have gotten three different jobs with three quite different websites. That is why I have not been blogging, as I have been quite busy writing content for these various websites.

So, I decided that I will list them here (as well as under my recently published articles area), so that you all can keep tabs on my latest works without me updating my blog every day.

1) The first opportunity that came my way was through Twitter. I had been speaking to the owner and operator of a website for many months, and she came up with a brilliant idea – to have two people watch the TV show “Lost” from the very beginning, one that has seen the show before and one that has not. The website is called the Geek Girls Network, and I have become their very first male contributor 🙂

Now, in case you didn’t know, I have been a large fan of Lost since the beginning, so I was offered the role of the veteran in this little experiment – hence the name of the posts, “Lost for Veterans.”

The introduction to the posts can be found here, while the first post (covering the first half of season one), can be found here.

The posts will be updated every week or two, so check the website (www.geekgirlsnetwork.com) regularly.

2) The second job also came from Twitter, as a friend of mine re-tweeted that a website was looking for another writer to add daily content on a wide variety of nerdy topics (such as pop culture, movies, interesting stuff found on the internet, TV shows, video games, and much more). So, I applied, and after a few days of seeing what I could do, they hired me!

The website is called Nerdbastards, and you can check out the link below to look at my profile, and see all the latest articles I was written for the site. I write stuff every day, so please check back as often as you can, as there is something for everyone on the site.

Here’s the link: David Manly’s Profile

3) And lastly, as this job just began this past week, is a weekly science blog on the website LabSpaces. I had been communicating with the owner and operator for a while over Twitter, and when he re-designed his website, we came up with the idea of having weekly updated content from individuals with knowledge on a particular field. I was offered to write posts about zoology and ecology, which as you know my blog, are two great obsessions of mine.

Without a any hesitation, I accepted and I put up my first post yesterday regarding the effects of oil on wildlife in the Gulf region. Please give it a read, as it was an absolute pleasure to write. The link can be found here.

If I do not update my blog as often as I should, I apologize, but it will primarily be because of all the time spent doing these three jobs. So, if you’d like to know what I’m working on, check those three sites! And feel free to comment on any and all posts, as I really do appreciate your feedback.

Lastly, I must say, all three of these jobs were presented to me due to my presence on Twitter. For those people who said it was a waste of time, I say, “Oh, really?”

Black-footed ferret project COMPLETE

Posted by :David Manly On : June 13, 2010
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Category: Black footed ferrets, MRP

Sorry for the long delay between posts, but it’s gotten surprisingly hectic over here.

I’ve got a few things on my plate that are keeping me busy, and some will be posted here (as well as on other sites as well), so I will keep you posted.

But, I just wanted to direct you to a project of mine that began while I was finishing up my Master’s of Journalism degree. The project deals with the plight of the endangered North American black-footed ferret, a cute mammal that has been in danger for many, many years.

I decided to create a multimedia website devoted to discovering what happened to cause its classification of endangered, what is being done in the United States and Canada and what the future could hold for the magnificent animal.

Thanks to an intrepid young web-designer and all the fellow students and professors who helped me out with this project, it became something that I am immensely proud of.

So please, do go check out all the video’s, slideshows, text and photo galleries I have there … and learn about an animal that needs our help.

Check out: “Back from the brink: The story of the North American black-footed ferret.”

Lost in LOST

Posted by :David Manly On : May 27, 2010
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Category: lost, Series finale, TV shows

NOTE: If you do not watch LOST, or have not watched the series finale yet, please be advised that this post may not be for you.

If you follow me on Twitter, you know that I have been an avid watcher of the TV show LOST since the very beginning. I was amazed throughout the entire first season, slightly disappointed with the second, and was heavily disheartened by the third. But, when the third season ended with one of the best scenes, I once again dared to hope.

The fourth season got much better, and continued into the fifth. This last and final season, number six for the series, had its ups and downs, but changed up the formula in a very interesting way. And, last Sunday, it aired its final episode.

Recently, I re-watched the final episode and took notes to address some of the good, the bad, and the weepy sprinkled throughout the episode. Also, each segment will be divided by an important quote (in bold) from the episode.

And be warned, SPOILER ALERT!

For my re-watch, since I already knew the ending to the story, I was able to keep an eye out for some references that didn’t occur to me during my initial watch, but gently hinted at the stepping stone answer.

Firstly, the ending has been discussed by countless people and will continue to be debated for a long time to come. People have praised it, and people have chastised it, but you all have to appreciate what they did. This is my attempt to explain it to those of you who are confused (I will get to the rest of the episode in a bit).

I’ve been told lots of random theories about the ending from friends, and this is my take on what makes the most sense.

Jack – “There are no shortcuts, no do-overs. What happened, happened. Trust me, I know. All of this matters.”

The quote speak volumes. Just like they did with the nuclear bomb explosion at the end of the last season, they could NOT simply re-do the timeline and forget everything that we had seen on the island. Everything that happened on the island was important to their growth as individuals.

One of the most important things to realize about the flash-sideways, is that TIME is RELATIVE.

Just because we were seeing them all together at the same time as the “present” time on the island, does not mean they were happening simultaneously. With the flash-sideways universe (much better name than purgatory or way-station or stepping stone in my opinion), time no longer matters to you. When you die, time ceases to exist.

While Jack died in the forest, many survivors of Oceanic flight 815 lived many years and died at their own time. One example clearly illustrates this from when Ben and Hurley were talking at the church.

Hurley – “You were a real good number two.”
Ben – “And you were a great number one, Huge.”

This hints that they lived many years after Jack’s final moments on the island, perhaps even centuries after.
NOTE: It has been revealed that on the complete series box set, there will be a special feature (about 10-14 minutes long) about the Ben and Hurley years on the island

Another note on the ending – I would have preferred someone else in the Deus Ex Machina role, other than Christian Sheppard. I believe Desmond, as our guide through the time-space continuum, would have been an amazing fit.

But, that said, the conversation between them in the multi-faith church (did you notice all the faith symbols scattered across the room and in the stained glass window? See the picture above) had a lot to cover and I thought they did it relatively well. It involved a lot of careful wording to let the audience know what was going on, and while they painted with broad strokes as to not focus on any religion to much, it was a little heavy handed at times.

Here’s the entire church conversation between Jack and Christian for you to examine:

Christian: Hello Jack.
Jack: I don’t understand. You died.
C: Yeah. Yes I did.
J: Then how are you here right now?
C: How are YOU here?
J: [realization hits] I died, too.
C: That’s OK. It’s OK, son [hugs]. I love you son
J: I love you, too, Dad. Are you real?
C: I sure hope so. Yeah, I’m real. You’re real, everything that’s ever happened to you is real. All those people in the church. They’re all real, too.
J: They’re all dead?
C: Everyone dies some time, kiddo. Some have been before you, some long after you.
J: Why are they all here now?
C: There is no now, here.
J: Where are we, Dad?
C: This is a place that you’ve all made together so that you could find one another. The most important part of your life was the time that you spent with these people. That’s why all of you are here. Nobody dies alone, Jack. You needed all of them, and they needed you.
J: For what?
C: To remember, and to… let go.
J: Kate… she said we were leaving.
C: Not leaving, no. Moving on.
J: Where are we going?
C: Let’s go find out.

What I think you need to take from all of this, is that the theme of this season was all about letting go and moving on. Think about that for a second: Letting go, and Moving On.

Every main character from season one let go of their personal baggage and was able to move onwards. These are only the main Losties who were at the church in the end and were characters from season one onwards.

Sawyer – Killed the real Sawyer and found love
Sayid – Embraced who he was and found redemption in love
Kate – Finally stopped running, and found love
Hurley – Found his purpose (helping people) and found love
Locke – Finally accepted that which he could not change and accepted help
Jack – Embraced his destiny and his true purpose, and yes, found love
Charlie – Embraced his destiny and found love
Claire – Embraced motherhood and found love
Sun – Became a more independent and self-sustaining woman, and re-affirmed her love
Jin – Realized that work was not all the was to his life, and re-affirmed his love

**I am not including Shannon or Boone, as their story lines were not as prevalent as the others**

Do you see a pattern there? Love. While it may not necessarily be romantic love, but I think it is more about a connection. To be “woken up,” it needs to be done by someone who had a profound impact upon your life.

These awakenings caused a lot of crying by millions of people. Therefore, here they are in order (for those interested).

1) Sun and Jin remember in the hospital
2) Sayid and Shannon in the alley
3) Kate, Charlie and Claire giving birth to Aaron
4) Locke in the hospital moving his toe
5) Sawyer and Juliet at the vending machine
6) Locke and Ben outside the church (not an “awakening,” but still very moving)
7) Hurley and Ben outside the church (also not an “awakening,” but very emotional)
7) Jack and Christian

Desmond – “No one can tell you why you are here but you”

Now, here are a few unanswered questions from the finale that were quite obvious to me upon a second viewing.

– Did everyone when they were “awakened” remember their deaths?
– Was Richard indeed ageing (remember the grey hair?) because of Jacob passing on his duties to Jack?
– How did Lapidus survive being struck by a large door underwater in a submarine, make it to the surface on pontoons and wait for rescue for a day or two?
– How did Boone “awaken”?
– How did the cave turn the Man in Black into the Smoke Monster, if he was unconscious (or dead) and all that is down there is a pool with a cork in it?
– If Eloise in the flash-sideways universe knew that it was a type of purgatory, why didn’t she leave when she “awoke”?
– Why didn’t Miles, Farraday or Charlotte “awaken”?
– Why after Jack and Smoke-Locke’s battle did it suddenly stop raining?
– Why didn’t Jack bless the water in the Oceanic bottle before giving it to Hurley (like Jacob did for him, and his mother did for Jacob)?
– Wouldn’t Richard be more terrified by being on an airplane for the first time in his life?
– Why did Kate change from her dress at the concert (and the one she was wearing in the car with Jack), to another one in the church?

Hurley – “It takes as long as it takes.”

With all those answered question from the finale, and all the countless mysteries that were left unsolved (there are tons), what did I think?

I believe that Lost ended the only way it could have – focused on the characters. Every main character had a few moments in the massive finale, and saw their personal stories get resolved before moving on.

Do not get me wrong, I love science fiction and was thrilled when they introduced time-travel, alternate universe, etc… into Lost. But, what you always must remember, is that Lost is a show about people. Granted, the people are in rather bizarre situations on an island with killer black smoke that can assume the form of the deceased.

One final note – for those who watched in the U.S. or did not see ads for what was coming up next on television, your probably saw something like this:

It was released yesterday that it was NOT planned by the producers or creators of the show. The final shot was supposed to be on Jack’s eye, and that was it. The images of the Oceanic flight wreckage was placed their by ABC executives to give viewers a chance to collect themselves and think before the news. These shots, however, let some people to believe that no one survived the initial place crash and the entire thing was a lie.

It was not their intention, just an ill-fated decision by ABC executives. It all still happened.

With all the good, bad and mysteries left unexplained, Lost was still a very impressive show. But, it was not perfect and they did stumble quite a few times … remember Jack’s tattoo episode?

Still, it was a hell of a ride.

David
The definitive host