alexbiojs

An amateur scientist (biology, JavaScript, linguistics, music) searching for rationality

This contest is an attempt to promote scientific knowledge among community in a fun and interesting way with the help of molecules.

Some people like to travel around the world and tell others stories about what happens outside of our organisms/cells in other countries.

And with “Identify the molecule” contest you can try to travel inside our own organism/cells and cells of the organisms around us.

For more information about this contest read “Identify the molecule” league. Prize: knowledge + 5/10 XRP + 200/400 TMN post.

Prizes/bonuses:

The prize here is

1. knowledge

facts, information, and skills acquired through experience or education; the theoretical or practical understanding of a subject

[Oxford Dictionary of English, 3rd Edition, Oxford University Press, 2010]

That understanding of our own organism and organisms around us is the real prize in the case of this contest. No matter what happens (whether or not you get 5 XRP), you can win (can acquire the knowledge by investigating different sources of information, remembering and using it to your advantage in the future).

2. 5 /10 XRP

3. 200/400 TMN

Aside from XRP I’d like to add TMN tokens.

For the uninitiated, TMN is the token of TranslateMe project (it’s about combining blockchain technology (NEO in this case) with translation industry).

The reason I’m going to add this token for the prize pool of this contest is not only because I have them, but because this contest is quite scientific, and TranslateMe project might help to solve the “lost” science problem.

For more on this you can read my post regarding TranslateMe (TranslateMe (or Decentralization meets Translation industry). Part 2. The “missing puzzle piece” of scientific ecosystem. General overview) (and other posts of that series).

For more information on crypto-bonuses for this league, please refer to “Identify the molecule” league. Prize: knowledge + 5/10 XRP + 200/400 TMN post.

Consider these tokens as a bonus.

Images and text are the clues for you to guess a riddle (the name of the molecule in this case).

Note that

a) even though this contest is called “Identify the molecule”,

-> molecule (singular)

sometimes it’s not just a molecule which is responsible for a specific function, but rather a complex of molecules.

Example:

cytochrome c oxidase (Complex IV)

is a large transmembrane protein complex… It is the last enzyme in the respiratory electron transport chain of cells located in the membrane.

source

b) some molecules/complexes have different names. For example, other names for cytochrome c oxidase (example above) are

Complex IV (mitochondrial electron transport). Cytochrome a3. Cytochrome aa3. Cytochrome oxidase. Warburg's respiratory enzyme.

source

Any of those names would be a valid entry.

c) Some almost identical molecules are grouped into classes / groups / families.

Example:

Helicases are divided into 6 groups. RecD and Dda molecules belong to helicases group (Superfamily 1 (SF1)). In this case you would need to guess only the name of the group –> Helicase/ Helicases.

d) Some proteins can have different forms – isoforms.

Example:

There’re trypsin 1 and trypsin 2. In this case you would need to guess only the general name – trypsin.

Important

In order to get TMN, you’ll need to have NEO-wallet and provide me your public NEO-address.

If you don’t have it yet, don’t worry, I published a post on how/where to get it (O3 wallet).

Note that NEO-addresses provided by exchanges will not work in this case (+ it's safer NOT to keep your funds on exchanges). It's highly recommended to get O3 wallet.

If there’re no winners on any stage, the prize will be distributed equally among all users who provided any guesses for molecules.

Rules (changed a bit)

This contest lasts for 6 days.

The change is that from now on, you need to provide your answers on Twitter, not on Telegram group.

The reason is that Twitter provides all the features needed and xrptipbot allows to tip users there.

So, it would be easy for me to distribute the prizes.

But you can still to use the Telegram group if you want to discuss the molecule, give suggestion for the league or something.

You'll find my posts here on Twitter

Leave your guess (1 guess only) in the reply to my twit with the riddle on Twitter.

Don’t edit your comment/reply and don’t provide any evidence that your answer is correct.

The first user with the right answer is the winner.

I’ll provide the answer in the Telegram group, will update this post and will let all the participants know it on Twitter.

Some of the clues have already been provided in the post.

Additional clues will be given in 2 days (on Monday, March 2, 2020, 20:00 ± 2 minutes UTC) (I’ll update this post).

And the rest of the clues will be provided in 2 more days (on Wednesday, March 4, 2020, 20:00 ± 2 minutes UTC) (I’ll update this post).

The reason is that some people might need less information to make conclusions that the others.

Additional clues will be added at the end of the “Riddle” section before the “Rules” section with “Edited” label.

The winner will be announced in the Telegram group/in this post on Coil and on Twitter (+ I'll publish a detailed review of the riddle after a while) on Friday, March 6, 2020, 20:00 ± 5 minutes UTC, so it's recommended to check that group on the 6th day.

I'll distribute the XRP prize via tipping on Twitter.

I’ll transfer the tokens (XRP + TMN) (if the winner provides me his/her NEO-address) to the winner on that day (March 6) and add the transaction ID (for TMN) in the Telegram group / on Twitter

I’m planning to run this contest every week.

So, you should expect to see the 9th week’s riddle for March on Saturday, March 7, 2019, 20:00 ± 2 minutes UTC.

The riddle goes below.

Read more...

https://www.youtube.com/watch?v=DDbfBrjMehQ

(header image source (Photo by Annie Spratt on Unsplash))

https://www.cinnamon.video/watch?v=262289793721828370

This was my first contribution to Open Mic contest (run on Steem) and my first video ever uploaded to somewhere.

I played quite famous “Oginski's Polonaise”.

It was written by Polish composer Michal Kleofas Oginski (1765 – 1833) in 1794.

Polonaise is

a slow dance of Polish origin in triple time, consisting chiefly of an intricate march or procession

[Oxford Dictionary of English, 3rd Edition, Oxford University Press 2010]

As a genre it’s known beginning from the XVIIth century.

They believe that Oginski wrote it while leaving Polish–Lithuanian Commonwealth, that’s why it’s also known as “Farewell to Homeland”.

Read more...

In this post I’d like to discuss the upcoming possible breakthrough in translation industry which might be achieved by leveraging the blockchain technology.

(cover image source – Pixabay)

As it was mentioned in the previous post, one of the problems of today’s science is “lost” science.

It refers to the situation when scientific discoveries get “lost” because of language barrier.

For example, this happened to the findings regarding bird flu virus strain called H5N1 which indicate that the virus also can infect pigs.

> The findings became widely known only when an author on the papers, virologist Chen Hualan of Harbin Veterinary Research Institute in northeast China, presented them at the International Symposium on the Prevention and Control of SARS and Avian Influenza in Beijing on 20 August. The results, which show that the virus was found in 2003 in pigs in southeast China, were originally published in January (L. I. Haiyan et al. Chin. J. Prev. Vet. Med. 26, 1–6; 2004).

(Bird flu data languish in Chinese journals [1])

That delay in a half a year with translation of the findings of Chinese scientists could become the reason of substantial human (and animal) loss.

There’s a dilemma of English being the lingua franca of today’s science:

a)

English is considered as the language of international communication in science. By the way, it was not always the case. Near 100 years ago, German would have this status. And it would probably not lose it, if there had been no world wars.

> The names of David Hilbert, Albert Einstein, Max Planck, Emil Fischer, Fritz Haber, Robert Koch and Rudolf Virchow would loom even larger, and German would probably have become the lingua franca of science—or rather, Naturwissenschaft.

Most of the ground‐breaking and classic papers in quantum physics were published in German.

(On science and English [2])

So, in order to publish your research in the high‐profile international journals and reach a wide audience, you need to present you results in English.

b)

On the other hand, while it’s important to communicate your findings in English, it’s also important to use other languages to do scientific discoveries.

Why?

As it was mentioned in the previous post,

> the even worse news is that right now, almost everything we know about the human mind and human brain is based on studies of usually American English-speaking undergraduates at universities. That excludes almost all humans, right? So, what we know about the human mind is actually incredibly narrow and biased, and our science has to do better.

(How language shapes the way we think | Lera Boroditsky [4])

Our language is the product of collaboration of our brain with environment. Languages are part of our culture. Given that the environment is different in various parts of the world, it shouldn’t be a surprise that languages might reflect reality around us in a different way.

The studies showed that the brain of the different language speakers works differently

> The critical difference in this case is not that English speakers cannot distinguish between light and dark blues, but rather that Russian speakers cannot avoid distinguishing them: they must do so to speak Russian in a conventional manner

(Russian blues reveal effects of language on color discrimination [3])

Russian speakers’ brain shows a surprised reaction during colour change, while the English speakers’ brain doesn’t.

In other words, given that the brain of different language speakers works differently, we might say that they perceive the reality differently. So, the more different language speakers deal with a particular scientific (and non-scientific) problem, the more chances are there to solve it. And I suppose, the more languages an individual knows, the more chances he/she has to solve his/her life problems (that knowledge makes our mind fore flexible/creative).

And there’re more than 7,110 languages currently spoken across the world [4].

And I’d like to follow Lera Boroditsky’s (one of the main contributors to linguistic relativity theory) way of thinking, and consider our languages as “living things” (organisms).

And just like other organisms on the Earth, our languages might be in danger, which is what’s happening now

We're losing about one language a week, and by some estimates, half of the world's languages will be gone in the next hundred years.

(How language shapes the way we think | Lera Boroditsky [4])

So, it’s important for us to preserve that linguistic diversity. For more information on this you can read one of my previous posts.

Every time we lose a language, we lose a potential way to make our mind more creative in problem solving.

So, to summarize, the dilemma is that on the one hand scientists are enforced to learn English. On the other hand, it’s important to preserve the diversity of our languages.

Taking into account a huge amount of research articles produced per year (near 2 million), seems like it’s hard to expect from the global translators community to translate all that into at least 100 languages [5]. Seems like we couldn’t manage to do this without the help of machines…

That’s where TranslateMe comes in

(source – Pixabay. Just like the Moon is the satellite of the Earth, TranslateMe might become a “satellite” for science when it comes to knowledge internationalization)

It is

a network of people and machines

[source – whitepaper]

In a nutshell,

TranslateMe = Neural Machine Translation (NMT) + computing power + human input

The best thing about Neural Machine Translation is that the system can learn, and easily improve upon previous translations, if given corrections.

[source]

Well, there’s of course services like Google Translate.

What’s more, there’re such services like Microsoft Translator and DeepL Translator.

By the way, it was shown that DeepL Translator outperforms in the accuracy of translation tech giants like Google, Microsoft and Facebook and raised the bar for translations quality [6].

One of the reasons is that DeepL was launched by the Linguee team. The same team which is the owner of the Linguee service. It provides your access to a huge database of the multilingual corpora of texts created with the help of webcrawlers.

Well, I said that they raised the bar, but I suppose that TranslateMe can raise the bar even further.

Why?

TranslateMe is not the first solution which tries to combine human with machine power. Google Translate also allows you to correct translations.

What’s make TranslateMe different is that it’s powered by the bockchain (NEO).

And its advantages comes from there.

As you most likely know, there’re a huge amount of crypto-projects nowadays. And most of them (or all?) gives you a chance to be rewarded for your contributions.

That is the case with TranslateMe as well.

It gives a chance to be rewarded with TMN (TranslateMe Token) as translators, as all people (as long as you know at least 1 language).

You can try their MVP (Minimum viable product) in the form of Telegram Chat App right now (visit TranslateMe official web-site for more information and read one of my previous posts).

So, as opposed to Google Translate, with TranslateMe you can be rewarded ultimately with $ for your efforts. And, let’s admit that in our society (the monetary society) $ serves sometimes as a good way to motivate people. Among other advantages are

up to 90% reduction in cost to the user, complete privacy options and no restriction of use

[source]

To my knowledge, the main purpose of TranlsateMe is to create an API.

API stands for Application Programming Interface.

It’s an interface provided to use the service.

Just like web-site translation can be carried out with the help of Google Translate API, TranslateMe will provide its API as well. But it will be more powerful (with more languages supported (6,000+), cheaper and, I believe, with more accurate translation).

That API will be used to translate everything: web-sites, chats, comments on social media etc.

Heck, even blockchain-powered social platforms could use it to break the language barrier and be more productive, popular and accessible for people of different nationalities.

Now, let’s get back to the “lost” science problem.

Will TranslateMe solve the problem solely by using machines?

No, as it was mentioned a lot of times in their posts on Medium, machine translation will never become perfect. There will always be the need for human touch.

That’s why I’d say that with TranslateMe emergence translators will not lose their jobs, but rather translation industry will become more productive.

And given just the 2 million of scientific articles produced per year, I’d say that the global community of translators will have more than enough job to do.

What’s more, with TranslateMe translators will deal directly with clients without third parties which cut translators’ profits substantially.

In other words, TranslateMe just may make it possible to cope with translation of a huge amount of materials (not only scientific).

At the same time, all that translation activity (as on the chat apps powered by TranslateMe API, as done by translators with the help of other TranslateMe solutions) will help to preserve languages.

And translated materials and TranslateMe algorithm will serve as a great educational material for language learners, which, by the way, helps to solve another problem mentioned in the previous post (education).

Read more...

This contest is an attempt to promote scientific knowledge among community in a fun and interesting way with the help of molecules.

Some people like to travel around the world and tell others stories about what happens outside of our organisms/cells in other countries.

And with “Identify the molecule” contest you can try to travel inside our own organism/cells and cells of the organisms around us.

For more information about this contest read “Identify the molecule” league. Prize: knowledge + 5/10 XRP + 200/400 TMN post.

Prizes/bonuses:

The prize here is

1. knowledge

facts, information, and skills acquired through experience or education; the theoretical or practical understanding of a subject

[Oxford Dictionary of English, 3rd Edition, Oxford University Press, 2010]

That understanding of our own organism and organisms around us is the real prize in the case of this contest. No matter what happens (whether or not you get 5 XRP), you can win (can acquire the knowledge by investigating different sources of information, remembering and using it to your advantage in the future).

2. 5 XRP

3. 200 TMN

Aside from XRP I’d like to add TMN tokens.

For the uninitiated, TMN is the token of TranslateMe project (it’s about combining blockchain technology (NEO in this case) with translation industry).

The reason I’m going to add this token for the prize pool of this contest is not only because I have them, but because this contest is quite scientific, and TranslateMe project might help to solve the “lost” science problem.

For more on this you can read my post regarding TranslateMe (TranslateMe (or Decentralization meets Translation industry). Part 2. The “missing puzzle piece” of scientific ecosystem. General overview) (and other posts of that series).

For more information on crypto-bonuses for this league, please refer to “Identify the molecule” league. Prize: knowledge + 5/10 XRP + 200/400 TMN post.

Consider these tokens as a bonus.

Images and text are the clues for you to guess a riddle (the name of the molecule in this case).

Note that

a) even though this contest is called “Identify the molecule”,

-> molecule (singular)

sometimes it’s not just a molecule which is responsible for a specific function, but rather a complex of molecules.

Example:

cytochrome c oxidase (Complex IV)

is a large transmembrane protein complex… It is the last enzyme in the respiratory electron transport chain of cells located in the membrane

source

b) some molecules/complexes have different names. For example, other names for cytochrome c oxidase (example above) are

Complex IV (mitochondrial electron transport). Cytochrome a3. Cytochrome aa3. Cytochrome oxidase. Warburg's respiratory enzyme.

source

Any of those names would be a valid entry.

c) Some almost identical molecules are grouped into classes / groups / families.

Example:

Helicases are divided into 6 groups. RecD and Dda molecules belong to helicases group (Superfamily 1 (SF1)). In this case you would need to guess only the name of the group –> Helicase/ Helicases.

d) Some proteins can have different forms – isoforms.

Example:

There’re trypsin 1 and trypsin 2. In this case you would need to guess only the general name – trypsin.

Important

In order to get TMN, you’ll need to have NEO-wallet and provide me your public NEO-address.

If you don’t have it yet, don’t worry, I published a post on how/where to get it (O3 wallet).

Note that NEO-addresses provided by exchanges will not work in this case (+ it's safer NOT to keep your funds on exchanges). It's highly recommended to get O3 wallet.

If there’re no winners on any stage, the prize will be distributed equally among all users who provided any guesses for molecules.

Rules

This contest lasts for 6 days.

Given that I don't see a comments section on Coil, I set up a Telegram group for this league, so that you could leave your reply with the guess there.

Leave your guess (1 guess only) in the Telegram group.

Don’t edit your comment/reply and don’t provide any evidence that your answer is correct.

The first user with the right answer is the winner.

I’ll provide the answer in the Telegram group.

Some of the clues have already been provided in the post.

Additional clues will be given in 2 days (on Monday, February 24, 2020, 20:00 ± 2 minutes UTC) (I’ll update this post).

And the rest of the clues will be provided in 2 more days (on Wednesday, February 26, 2020, 20:00 ± 2 minutes UTC) (I’ll update this post).

The reason is that some people might need less information to make conclusions that the others.

Additional clues will be added at the end of the “Riddle” section before the “Rules” section with “Edited” label.

The winner will be announced in that group (+ I'll publish a detailed review of the riddle after a while) on Friday, February 28, 2020, 20:00 ± 5 minutes UTC, so it's recommended to check that group on the 6th day.

I'll ask to provide me there your XPR-address.

I’ll transfer the tokens (XRP + TMN) (if the winner provides me his/her NEO-address) to the winner on that day (February 14) and add the transaction ID in the Telegram group.

I’m planning to run this contest every week.

So, you should expect to see the 2nd week’s riddle for January on Saturday, February 29, 2019, 20:00 ± 2 minutes UTC.

The riddle goes below

Read more...

> The Brain — is wider than the Sky —

For — put them side by side —

The one the other will contain

With ease — and You — beside —

The Brain is deeper than the sea —

For — hold them — Blue to Blue —

The one the other will absorb —

As Sponges — Buckets — do —

(‘The Brain is wider than the Sky’ poem by Emily Dickinson)

You might be surprised to see that piece of a poem in the post titled like that (“Myths vs Reality. Christmas. Introduction”). A lot will start making sense soon.

(the overall image was created by me by combining the images from Pixabay, namely: Flying reindeers, Santa and a reindeer, An Elf, Christmas attributes)

Disclaimer (important)

If you’re a child (or Phoebe Buffay), the information given in the posts of this series can ruin/break your expectations regarding Christmas.

I will not have any responsibility for the consequences.

On the other hand...

Jacque Fresco (the one who believes that it’s our environment which determined the way we behave) mentioned a lot of times that the kind of a child you get depends on the environment you “feed” him/her with.

The childrens' capabilities are usually underestimated.

That’s why there’s “Biochemistry Literacy for Kids” project.

> Unlocking the true potential of young learners.
Biochemistry Literacy for Kids revolutionizes STEM learning by making college-level science accessible to K-12 students. Developed by Yale-educated chemistry professors, our curriculum creates a unique visual and tactile learning environment that makes high-level chemistry and biochemistry fun and rewarding for kids as young as age 6.

(source)

Prologue

In this post I’d like to talk about Christmas, well-known religious holiday celebrated by billions of people all over the world.

Christians number 2.2 billion, or about one-in-three (32%) people worldwide.

((source) – [1])

While being the major Christian holiday, Christmas is a tradition not only for religious people, but for non-religious people as well [2].

The latter consider it as a chance to spend more time with their family, exchange gifts, dance and have fun. For children it is usually associated with Santa Claus coming into the house through chimneys with gifts, flying reindeers etc.

I’d like to try to answer 2 main questions:

1. Where does the tradition/holiday originate?

2. Why have/How could we ended up in such a situation (having flying reindeers and Santa Claus…)?

While the answer to the 1st question could be illustrated with the help of just 1 image, answering the 2nd question will take a lot of writing. It’s because the answer should lie within our brain (its properties/features/capabilities), that “device” we all have.

(Andreas Vesalius' Fabrica, Base Of The Brain. Public Domain)

World views

There’s a number of so-called world views/world outlooks, namely (at least):

* mythological (think of Greek mythology)

* religious (think of Christianity, Buddha etc.)

* scientific

world view

is the way they see and understand the world, especially regarding issues such as politics, philosophy, and religion.

(Collins Cobuild Advanced Learner’s English Dictionary. New Digital Edition, 2008)

That world view depends on the environment we grown up.

People had very different world view several thousands years ago from what we have today.

Mythological, religious and scientific world views try to explain our world.

They try to explain what reality looks like. And they define how people will behave in different situation.

I’ve tried to explain why it’s hard to see the way thing are in the first post of this series.

The scientific view of the world seems to me the most realistic one, because it’s based on experiments.

a scientific procedure undertaken to make a discovery, test a hypothesis, or demonstrate a known fact

(Oxford Dictionary of English, 3rd Edition, 2010)

> But if you tell these kids that you have a special power, they don't work on problems.

See, if you prey and hope that it rains…

You have to dig an irrigation system to save you out of drought and help the plants to grow.

(Jacque Fresco. “Charlie Veitch interviews Jacque Fresco in London”)

Technology and Science is not the answer to all our problems.

But it has more answer than non-technology/non-science.

In fact, there’re so-called scientific revolutions (think of Copernican Revolution for example).

In a nutshell, at some point there’s quite a few anomalies in the current scientific paradigm.

This leads to new paradigm (paradigm shift, as per Thomas S. Kuhn's “The Structure of Scientific Revolutions” (1962)), the one which can explain those anomalies.

The theory

In this series of posts I’ll share the theory (which try to provide scientific explanation for Christmas-related events) which was told to me at the university I was a student of.

Please, note that it is just a theory. There’s no 100% guarantee it’s the truth. As I said in the Intro post of this series, it is really hard nowadays to figure out what the truth is because of a huge amount of misinformation.

Once I’ve heard the explanation (which is quite funny), suddenly everything about Christmas just started make sense. I believe at this stage of my life that there’s way too much coincidence between that theory and Christmas which are not accidental.

What's the plan?

I want to share the plan for this series.

To try to answer the above 2 questions, we’ll need to talk about metaphors, allegories, abstractions in the 1st post.

Then, in the 2nd post, we’ll talk about the thinking process itself trying to figure out how it even happens (does it happen with the help of images, language, or what?).

Then we’ll discuss the actual theory which tries to explain Christmas-related stuff.

After that I’d like to talk about biochemical foundation supporting the theory.

And, finally, I’d like to talk about the impact that Christmas has on our environment.

Metaphors, allegories etc.

An important role in this series will be played by metaphors.

> A metaphor is an imaginative way of describing something by referring to something else which is the same in a particular way. For example, if you want to say that someone is very shy and frightened of things, you might say that they are a mouse.

If one thing is a metaphor for another, it is intended or regarded as a symbol of it.

(Collins Cobuild Advanced Learner’s English Dictionary. New Digital Edition, 2008)

(Coil subsribers will get access to the information regarding the metaphor for this series of posts itself)

Other posts of this series:

Myths vs Reality. Introduction (or why it’s hard to see the way things are) (interdisciplinary short review)

Myths vs Reality #1 Vampires/Werewolves… Is there any scientific explanation?

Read more...

(or “Catch me (Cd2+) if you can”)

In this post we’re going to continue our “journey” with MKPs (MAP kinase phosphatases).

(DUSP2 catalytic domain (surface representation) with its conservative (V)-HC-XX-X-XX-R-(S/T) motif (highlighted with magenta). 3D-structure (PDB-file) – 1M3G in this case – was obtained from PDB. The image was created by me with the help of PyMol - open source tool for molecules visualization/exploration. You can use the image if you want).

Feel free to leave comments related to the topic of this post (or this series of posts). As I mentioned in the introduction post for this series, I’m not a professional bioinformatician/biochemist, so if you see any mistakes or have a question, go ahead.

Before we begin to investigate actually possible ways Cd2+ could “use” to influence MKPs (hence MAPK signalling pathway), let’s try to investigate Cd2+ relationship with MKPs using another approach. We’ve found out in the first part of this series that Cd2+ affects MAPK-signalling pathway [1].

Great. But MAPK signalling pathway is one of the best studied signalling pathways ever [2]. And you, probably, remember from the first part, how scary all that looks. What if we would like to narrow down the list of MKPs cadmium could have impact on, or what if we wouldn’t have the data we’ve got from the articles/papers/monograph. As it was mentioned in the first part, MAPK signalling includes MAPK kinase kinases (MKKK or MEKK), MAPK kinases (MKK or MEK) and MAPKs themselves [6].

Knowing what genes products exactly of the MAPK pathway are influenced by Cd2+ also would help us to understand, if Cd2+ could influence MKPs at all. Because if the list of genes/genes products influenced by Cd2+ includes all kinases except for MAPK themselves (which are the only ones (according to that image on KEGG) regulated by MKPs), then Cd2+ should not influence MKPs (what might dash our hopes for/ruin the whole idea of the first experiment).

We saw in the first part, that the range of DUSPs which can regulate ERK (also known as MAPK1) and ERK1 (MAPK3) ([3]) includes DUSP1, DUSP2, DUSP4, DUSP5, DUSP6, DUSP7, DUSP8, DUSP9, DUSP10 and, finally, DUSP16 (10 DUSPs in total).

And the range of DUSPs which can regulate JNK (also known as MAPK8), MAPK9, MAPK10 ([4]) and p38 (also known as MAPK14), MAPK11, MAPK12 and MAPK13 ([5]) includes all of the DUSPs above except for DUSP1 and DUSP6 (8 in total).

(the image is from Wikipedia. Public domain. MAPKs are highlighted with the green squares. When you hover over/click on ERK/JNK/p38 elements on KEGG we get a set of MAPKs. That's how we get the MAPKs groups you can see on the right. The image was modified by me. You can use it if you wan).

(the image is from Wikipedia. Public domain. The parts of this image with better resolution is below. I placed this, so that you could get an overall picture of MAPK pathway. Mitogen-activated Protein Kinase Phosphatases (MKPs) are highlighted with the blue ovals. When you hover over/click on MKP element on KEGG we get a set of DUSPs. That's how we get the DUSPs list you can see on the right top corner. The image was modified by me. You can use it if you wan)

Well, it doesn’t look like a big difference (10 or 8), but imagine if the difference in your particular case with another signalling pathway and proteins was something like 7 and 54 for example.

So, let’s try to narrow down that list of MKPs we might be interested in (and again, we’re interested in those which could be somehow indirectly (or directly) affected by Cd2+.

The logic here is as follows:

If we know what MAPKs genes/genes products exactly of those mentioned above are influenced by Cd2+, we could narrow down the list of MKPs (or, if no MAPKs genes get activated, then we could exclude the possibility that Cd+2 could influence MKPs at all (which would actually dash our hopes and the reason to do all this first Exp.)).

Of course, we could try to analyze the literature (dozens of papers/articles) searching for the answer – what MAPKs exactly are influenced by Cd2+ (and again, if they are influenced by it at all). But, as it was said in the introduction of this series of posts, bioinformatics might help us to save a lot of time. So, let’s leverage its power and try to figure out what MAPKs/MKPs genes are influenced by Cd2+ by carrying out ontological analysis.

Also, probably, there’s just no such information in the literature yet (what MAPKs are influenced by Cd2+), but it might be in the databases developed for biologists/bioinfomaticians.

And, finally, some literature (especially monographs) might just cost a lot (and all databases, I’ve seen so far, were freely available).

Now, let’s try to figure out what ontological analysis is. But before that let’s try to figure out what ontology is. In the philosophical context it’s the study of being (answering the questions like “What is existence?”, “What does it mean to exist?”) [7].

The best definition I could give with my own words as for now for “ontology” in the context of science is

Ontology is the group of concepts/ideas/terms we should use to describe something, which help us to organize information into knowledge and exchange it [8].

And Gene Ontology (GO) is an initiative/project which deals with, obviously, genes and genes products, and tries to provide scientists those concepts/ideas/terms. For example, it provides vocabulary we should use to describe proteins (so that scientists could unambiguously understand each other). And those concepts/ideas/terms are grouped into 3 main fields: cellular component, molecular function (that gene products do) and biological process (where those products participate) (so that we have 3 ontologies). Each term has a unique identifier, and all terms are organized into a hierarchical structure (graph) (with parent-child relationships) [9, 10].

All this stuff is provided by Gene Ontology (GO) Consortium.

And then all that is used by Gene Ontology Annotation (GOA) project to annotate (document) genes products as manually, as electronically/automatically.

We (biologists) might get access to all that (ontological terms (provided by Gene Ontology (GO) Consortium) and annotations (provided by Gene Ontology Annotation (GOA))) with the help of web-interface – QuickGO browser for example (kind of Google search for bioinformaticians) [11].

(The image was created by me. The question mark was taken from Pixabay. Pixabay License)

And, finally, I could describe ontological analysis as the process of finding information about genes/genes products using those ontologies/web-interfaces.

Anyway, all this should become much clearer in practice.

Getting the list of genes related to the cellular response to cadmium ion

What we are going to do now is to go to QuickGO website and search for “cadmium” [14].

What we are interested on results page is “cellular response to cadmium ion” term (you’ll see a button saying “2,008 annotations” (February, 2020).

Click that button and wait for results. Now, you can click “GO terms” button. There you’ll see “cellular response to cadmium ion” with an icon (parent-child relationship), click that icon.

A special modal window will appear with the hierarchical structure indicating where “cellular response to cadmium ion” (GO:0071276) term is located.

Then you can click on it, and a page dedicated specifically to that term will be opened. On that page you can see that this term has child terms like “cellular detoxification of cadmium ion” and “SCF complex disassembly in response to cadmium stress”. Also you can see a clear definition for “cellular response to cadmium ion” term. We chose “cellular response to cadmium ion” result on that QuickGO results page for “cadmium” search, because it’s the most common term (parent) in our case (well, it’s almost the most common term, because we also can see “response to cadmium ion” term as its parent but we are interested in “cellular response”).

Now, click “Taxon” button on the page with annotations for “cellular response to cadmium ion” term and choose “Homo sapiens”, click “Apply” (at the bottom of the modal window). As a result our 2,008 annotations narrow down to 59.

Now click an “Aspect” button and choose “biological process” option and click “Apply”.

As it was mentioned above genes products can be annotated manually (by experts) and automatically (by computers). Now click an “Evidence” button. There you can choose the evidence code you need. For more information on this go to geneontology [12].

Well, I used QuickGO several years ago. At that time there was an “Inferred from Electronic Annotation (IEA)” option in that “Evidence” window [13]. So, as far as I understand, now that option is not there, and according to QuickGO FAQ page “All manual codes” higher-level grouping (the parent for all manual annotation evidence codes) has an ECO:0000352 (“evidence used in manual assertion” in our “Evidence” window). So, we can just choose that to include all manual annotations. Then click “Apply”.

But if you would want to also see annotations added by computers automatically, then, as far as I understand, you need to add an “Inferred from Electronic Annotation (IEA)” option (with “add” button in the “Evidence button”).

After applying all those filters we now have just 42 annotations.

All we have to do now is to export our data. But before that let’s click “Customise” option. In the window appeared let’s leave just “Symbol” and “Evidence” options. Click “Customise” again to remove the window.

Finally, click “Export” button, choose “Tab-delimited” (tab-separated values/TSV) format and click “Go”.

|| Useful tip

Now, if you open the exported file with .tsv extinction with Excell, you’ll see that all your results are located in just 1 cell (it’s just a chaos). But, if you open that tsv-file in Notepad, copy all the data there and paste them into that same Excell, you’ll see that all pieces of the data are in separate cells. Looks like by copying data initially to Notepad we remove some formatting information.

And finally we have a list of genes (“SYMBOL” column) (we see 42 genes, but there are just 29 unique genes) related to “cellular response to cadmium ion”. And we can already see MAPK1, MAPK3, MAPK8 and MAPK9 among them.

( The image above shows the part of the list of genes related to the “cellular response to cadmium ion” term. The genes were taken with the help of QuickGO. The image was created by me. You can use it if you want)

In the next part (Part 3. B) we're going to find biological processes in which the genes we've got in this post are involved in with the help of GeneCodis and discuss in detail results of all we've done in this (3rd) part.

Other posts of this series:

Bioinformatics experiments. Introduction

Bioinformatics #1 The analysis of Cd2+ impact on MAPK-signalling through DUSPs. Part 1. Theory

Bioinformatics #1 The analysis of Cd2+ impact on MAPK-signalling through DUSPs. Part 2. MSA (Multiple Sequence Alignment)

References:

1. Sigel, Astrid, Sigel, Helmut, Sigel, Roland K. O. (Eds.). Cadmium: From Toxicity to Essentiality. 2013, XXXVI, 560 p. 128 illus., 43 illus;

2. Casar B, Crespo P. ERK Signals: Scaffolding Scaffolds? Front Cell Dev Biol. 2016 May 31; eCollection 2016. PubMed PMID:27303664; PubMed Central PMCID: PMC4885846

3. MAPK1/MAPK3

4. MAPK8 / MAPK9 / MAPK10

5. MAPK11 / MAPK12 / MAPK13 / MAPK14

6. Lawrence MC, Jivan A, Shao C. The roles of MAPKs in disease. Cell Res. 2008 Apr;18(4):436-42. doi: 10.1038/cr.2008.37. Review. PubMed PMID:18347614

7. Ontology

8. Ontology (information science)

9. Gene ontology

10. Huntley RP, Binns D, Dimmer E. QuickGO: a user tutorial for the web-based Gene Ontology browser. Database (Oxford). 2009;2009:bap010. Epub 2009 Sep 29. PubMed PMID: 20157483; PubMed Central PMCID: PMC2794795

11. Binns D, Dimmer E, Huntley R. QuickGO: a web-based tool for Gene Ontology searching. Bioinformatics. 2009 Nov 15;25(22):3045-6. doi: 10.1093/bioinformatics/btp536. Epub 2009 Sep 10. PubMed PMID: 19744993; PubMed Central PMCID: PMC2773257

12. Guide to GO evidence codes

13. Inferred from Electronic Annotation (IEA)

14. Binns D, Dimmer E, Huntley R. (2009). QuickGO: a web-based tool for Gene Ontology searching. Bioinformatics. 2009; 25(22):3045-6

PublishOx is a fantastic publishing platform with a number of cool features.

The most important features is probably the fact that it is a crypto-agnostic platform (which means it doesn’t have its own token, but rather use the tokens provided by other crypto-projects), which makes it immortal to some extent, and that it allows to earn writers as well as readers.

I’d like to put into this tutorial some creativity.

(the overall image was created by me. All the characters/objects were taken from Pixabay, namely:

crown, clew, birds, castle on the right, castle in the middle, pigeon, tower, fluite, crossing sign, farmer, fox, flutist, izba, bag, map, owl, firebird, squirrel, prince, castle on the left, witch, trolley, coffers (with gold))

For that, I’d like to provide a set of metaphors and personifications which will allow to create an allegory related to PublishOx.

But first of all, I think I need to talk a bit about all those strange (for some users) words in the previous sentence.

metaphor

If one thing is a metaphor for another, it is intended or regarded as a symbol of it.

[Collins Cobuild Advanced Learner’s English Dictionary. New Digital Edition, 2008]

personification

the attribution of a personal nature or human characteristics to something non-human, or the representation of an abstract quality in human form

[Oxford Dictionary of English, 3rd Edition, 2010]

allegory

Allegory is the use of characters and events in a story, poem, or painting to represent other things.

[Collins Cobuild Advanced Learner’s English Dictionary. New Digital Edition, 2008]

So, in a nutshell, metaphors and personifications allow us to encode some abstract information (like faith, liberty etc.) into characters/objects (something which we can see). Then we can create a story (allegory) with the help of them.

Why would we even want to do this?

Well, the thing is that

the view on metaphor has been transformed from it being something poetic reserved for literary use, to something fundamental and generalizable in our daily language and thinking (Lakoff and Johnson, 2003). The pervasiveness of metaphors has been quantified: People use about 5 metaphors for every 100 words of text (Pollio et al., 1990), including 1.8 novel and 4.08 frozen metaphors (e.g., leg of a table) per minute of discourse (Pollio et al., 1977).

(source – [1])

Metaphorical way of thinking is deeply hardwired into our brain.

Metaphors help us to understand and remember something better.

Just think even about crypto-tokens which are represented as coins or crypto-wallets which allow to get access to them (they say that a better metaphor would be a window rather than the wallet because it allows to get access to your funds (not to put the crypto in the wallet like we do with general wallets) for more on this later). They are metaphors as well, and they help people to grasp the idea of the crypto better (without the need to go into technical details).

The thinking itself (according to some theories) happens with the help of images (2D/3D) [2].

That’s why in this tutorial I’d like to represent/encode different aspects of PublishOx into characters/objects of Slavic folklore in order to create and tell a story/narrative.

And the cool thing about stories is that

Stories up to 22 times more memorable than facts alone

(source)

Jennifer Aaker (Professor of Marketing at Stanford Graduate School of Business)

So, let’s go.

To give you an idea of what I mean by Slavic folklore, you can watch the following fairy tale called “Иван-царевич и Серый волк”

https://www.youtube.com/watch?v=fUpXNUpbuZQ

Here it is on Wikipedia

In a nutshell, Tsarevich Ivan is a son of a king. He needs to do some tasks for his dad (like finding a firebird (and bringing it to the kingdom of his father) and travel to another kingdom.

This is the story I’ll use (with a lot of modifications) to create a fairy tale about PublishOx.

The user of PublishOx will be represented as Tsarevich Ivan. And he/she will travel to PublishOx kingdom to do some tasks, get some rewards etc.

You can think of all this as** a computer game** where you are the main character, you have some objects/skills and you have some missions to do to get/achieve something.

You, probably, heard that users joining different social platforms say in their Introduction posts sometimes that their journey begins.

In the case of this tutorial it is going to be a journey in a literal sense.

Below you’ll see the image with whole story represented.

Right now it might seems crazy and non-sense.

But this all will start making sense soon.

So…

In the context of PublishOx kingdom you can be (in no particular order)

1. content creator;

2. A web-site owner (PublishOx provides you an opportunity to use their widget which helps to turn your web-site into Publish0x-friendly one)

3. An Ambassador;

4. A reader;

5. One of the PublishOx Team;

6. A Sponsor/Advertiser (those who give crypto to PublishOx team to form a rewards pool for users)

Here’s metaphors for the aforementioned roles:

(the overall image was created by me. All the characters/objects were taken from Pixabay)

Please, note that the Dragon (which is quite often used in Russian folklore as Koschei) despite his look play a number of positive roles in fairy tales.

The user

The user (Tsarevich Ivan) of PublishOx can be a Content Creator, Web-site Owner or an Ambassador.

(the overall image was created by me. All the characters/objects were taken from Pixabay)

Note that the user is represented as Tsarevich Ivan, it’s just the roles he can play (and the skills he can demonstrate) are encoded as a farmer (Content Creator), a flutist (Ambassador) and a crown (Web-site Owner).

So, let’s consider the 1st piece of the image.

At the beginning of your journey I’d suggest to think about the wallet you’ll use.

Metamask

Note that I’ll talk Metamask in this case. Metamask is represented as a fox with a bag.

Currently PublishOx supports only Ethereum-based tokens.

(the ball image was taken from Pixabay)

Note that we will not store tokens in the bag. As it was mentioned above, a better metaphor for a wallet would be a window, so we’ll use a crystal ball (that is used by witches to predict the future or to know what’s going on in different parts of the world; just like that, so-called wallets help to see what happens on the blockchain, well, and they help to do some actions with your assets) which will be stored in the bag.

By the way, note that Metamask developers use the fox as a symbol (don’t know if it has any metaphorical meaning, though) for their program. And a lot of other software programs are associated with animals or objects because it help to remember the product.

For more details, please, see the video below.

The clew you see near the Tsarevich Ivan is used in fairy tales as a tool to help the characters to navigate/to find the right direction. Just like that, PublishOx support resources (Telegram, support@publish0x.com, FAQ) is the best way to navigate throughout the PublishOx kingdom in the right direction.

Once you’re done with Metamask, you’ll need to register on PublishOx (which you can do at the home page (“Sign up & Earn crypto” button) and be approved as an author by the PublishOx team (but, of course, you can register without Metamask as well).

The journey starts (see the green number 1) when you move from your own kingdom (see the castle on the left), crossing the border, to the castle of PublishOx kingdom (on the right) (see the green number 2).

That’s where you can “negotiate” your application as an author with PublishOx team (which is represented as the black Dragon with yellow eyes).

Ambassador program

To join an Ambassador program and get the Website widget you‘ll need to go to Dashboard.

The castle on the right represents the part of PublishOx interface with the Dashboard.

The castle on the right represents the part of PublishOx interface with the Dashboard.

That’s where you can

a) create the widget

which is represented on the image as a firebird, because when you bring it to your house/castle it light up, so that your environment gets styled in a way defined by the properties of the firebird. Just like that, PublishOx widget helps to make your web-site look in PublishOx style.

For more details, please, see the video below.

b) get your ambassador link and TIDs (Tracking IDs)

Once you have it, you can add it to the URL-address of the posts you share to get some rewards.

For more details, please, see the video below.

The Ambassador role is represented as a flutist (see the green number 3) because flutists (and other musicians) share their music (and stories) with the audience. Just like that, you will share URLs with people on different platforms to attract potential users to PublishOx. Also you can see apple trees (top right). That’s the potential content flutists could attract to PublishOx.

So, now you have Web-site widget (represented on the image as a firebird), Tracking IDs (necessary for Ambassador role).

Lets’ move on.

As a content creator you will be represented as a farmer (see the green number 4), because it’s a farmer who plants trees (apple trees and oak trees in our case) which give crop (apple/acorns in our case used as a metaphor for our content/posts) consumed by other people and animals (just like readers read/consume content on PublishOx). Note that PublishOx allows us to create several blogs (different trees (apple trees and oak) represent different blogs created by the user).

Readers (consumers of the content) will be represented as animals (squirrels and birds who eat acorns and apples).

Editor

To write a post on PublishOx you’ll use an Editor (see the green number 5).

It’s represented on the image as an izba because that’s the place where the Baba-Yaga (witch in Russian folk-tales) lives (who flies with the help of a broom; top left).

Baba Yaga usually helps characters in fairy tales to get some tools they will need in their journey.

And the Editor is actually a set of different tools for editing.

As for free images and music sources, I’d recommend:

for images:

pixabay – https://pixabay.com/

unsplash – http://unsplash.com/

for music:

http://teknoaxe.com/

Welcome to TeknoAXE Royalty Free Music! All music hosted here is covered under CC 4.0. There are 1564 music tracks here and new music is added to this site every week.

(source)

That’s were I’ve got the music for the video-review given at the end of this post.

The end of the user’s journey is shown on the left.

That’s the place where he might have his own kingdom with the castle (his own web-site).

And that’s where the firebird (PublishOx widget) might come into play.

The role of the Web-site owner is represented with the help of the crown.

Tips model

Now, you plant the trees/grow the crop (like apples and acorns), great.

But where does the money come from?

Well, as it was mentioned at the beginning of the post, PublishOx is crypto-agnostic.

Their rewards pool is formed by the advertisers/sponsors.

Those projects get exposure in exchange for helping PublishOx with the rewards pool.

The readers can send the creators a tip with the help of a tool (tipper) located at the end of the post.

The tip is a micro-payment.

Now is the time to connect your Metamask ETH-address to PublishOx.

For more details, please, see the video below.

Note that when users tip you under your posts, that micro$ doesn’t go directly to your address on-line.

It seems more like an instruction for PublishOx team on what amount of their rewards pool should be allocated to you.

(that's why you see a separate coffer on top of the image below)

What was said above is summarized on the image below.

Sponsors (see the green number 7) give PublishOx their crypto (represented as coffers (with gold) moving to the PublishOx castle).

Information about the tips and $ received for the Ambassador’s role is transferred to the team. And that is represented with the help of pigeons.

To withdraw your funds you’ll need to go to “Payments” section in the “Dashboard” (once you have enough for withdraw feature to be activated).

Notifications feature

Now, there’s notifications feature on PublishOx. If someone follows you or publish his/her content you get notifications. That’s represented on the piece of the image below.

The notifications feature us represented with the help of owls that transfer messages (see the green number 8).

Content on PublishOx

Fine, finally let’s talk a bit about the content on PublishOx.

Well, it’s pretty clear that PublishOx is primarily for crypto-related content.

You can explore it with the help of “New”, “Popular”, “Explore” and other tabs (it’s pretty intuitive) (also you can just click crypto-icons on the top to get details about the project and content related to it).

That feature is represented by the tower on the top right (see the green number 9) because it’s a tower which helps to explore the horizons/environment.

Read more...

Note that this post is also a part of my other series called “Mnemonics (Memory Palace) experiments”

This is another example of using metaphors, allegories and personalities.

I believe that ScientificCoin has a potential to become one of the best dApps.

(image source)

I guess that calling something “the best” is quite subjective and depends on the one’s experience, interests etc.

I want to present (subjectively) criteria that I believe the dApp should meet to be the best.

It should

1. allow people to use their time effectively to solve important problems (and not to “kill” their time);

2. be unique;

3. be open source (ideally with the code placed on GitHub), so that the world community of programmers and other specialists (like translators…) could easily contribute;

4. be led by the team of experienced professionals;

5. be open for a wide audience (ideally, all people all over the world);

6. use innovative technologies to minimize the impact of the blockchain technology usage (like excessive usage of electricity);

7. have a positive impact on our society and environment;

8. have a good performance and User experience (UX);

In a nutshell,

ScientificCoin = science + blockchain

There’s a number of problems in today’s science, namely:

1. Funding of scientific projects/monetization of the skills provided by scientists;

2. Access to knowledge/information;

a) “lost” science. “Lost” because of language barrier. Not all articles/papers are accessible in English (the lingua franca of science);

b) “hidden” science. A lot of papers/articles are “hidden” behind the expensive paywalls;

3. Publishing. Some articles (even those worth the Nobel Prize like this article on graphene) aren’t published because of inadequate peer review process.

Take for example this article on graphene. It was rejected twice and took at least 1 year to get published. And then, in 2010, went on to win the Nobel Prize in physics.

[Open Science can save the planet | Kamila MARKRAM | TEDxBrussels]

4. Collaboration

Not only scientists could use GitHub-like platform for collaboration and making scientific data open to everyone, but they could probably set sort of bounties to complete some tasks/run experiments which they couldn’t do/run themselves (because of lack of appropriate equipment/materials).

5. Education.

Initiatives like MOOC (Massive online open courses) try to make education available for free for everyone.

To get more information about the problems (and their blockchain-based (and non-blockchain-based) solutions) you can read my posts:

Blockchain-Based Scientific Ecosystem (dExperiment is coming). General overview

And ScientificCoin tries to solve some of these problems.

In order to help you to understand and remember what ScientificCoin project is about, I’d like to provide an analogy based on the scenes of “Star Wars” series of films. It’s going to be kind of usage of mnemotechnics technique.

For the uninitiated, the basic idea of classical mnemotechnics is to encode information into images and place them into locations (that's why it's also called The Method of loci (the plural of locus)).

The idea might seem crazy, but a lot will start make sense towards the end of the post.

Well, obviously, “Star Wars” wasn’t initially designed to encode information about ScientificCoin project, so not everything about ScientificCoin will fit perfectly into “Star Wars” scenes.

However, it fits pretty well for this purpose.

Okay, let’s get started.

There’re 3 pillars of ScientificCoin project:

1. Crowdfunding platform;

2. Freelancing platform for scientists;

3. Monsterbrain (educational platform);

Note that ScientificCoin project is the work in progress. They haven’t developed all the features yet, but they have something to show you already. And ScientificCoin indeed is going to be a dApp with open source code published on GitHub (I asked this on their Telegram group).

What’s more, they have already 1 successfully funded project.

HealthMonitor (I’ll talk about it later).

1. The main problem ScientificCoin currently is trying to solve is fundraising/crowdfunding with the help of their

Here you can think about ScientificCoin project as Kickcstarter, but exclusively for scientific projects.

There’re 2 parties:

a) scientists with ideas, who need advertisement for their ideas/projects;

b) investors with $, who need a way to minimize the risks for their investments / a reliable way of scientific projects evaluation;

And ScientificCoin project is trying to provide both parties what they need – a platform for scientists to easily advertise their projects and for investors to provide them sort of rating of scientific projects.

The rating is determined based on 2 methods:

a) mathematical algorithm;

b) the wisdom of the crowd (the latter includes as people with scientific background, as people without it);

Now, let’s try to use “Star Wars” analogy to better understand/remember all this.

First of all, we need a scientific project (which in our case is going to be Anakin Skywalker).

And we have Jedi (scientists who a trying to bring the project to life; is our case it is Qui-Gon Jinn).

In our case, Anakin Skyworker (scientific project) needs some equipment (like a lightsaber (energy sword), cloth, etc.) from the investors of the Galactic Republic to be trained and become a Padawan.

(lightsaber image source)

In the contest of this post I'd like to encode investors into Senators of Galactic Republic

like the Queen Padmé Amidala of Naboo.

(image source)

First of all, projects creators have to fill a form. Information provided there will be used for mathematical algorithm evaluation.

You can find out how it looks like here (scroll down).

There're dozens of fields there you need to fill.

The project should be evaluated in order to get financing from investors. This happens in 2 stages:

a) mathematical algorithm;

In our case it’s The Force.

In the film it’s used for the things like reading thoughts, evaluating a person, moving objects etc.

ScientificCoin mathematical algorithm judges the projects based on near 70 different parameters of 5 categories [1].

Once the project gets evaluated by the algorithm, it gets a score

(image source)

b) “the wisdom of the crowd”

In our case it’s the Jedi Council

with a group of creatures (including humans) evaluating whether or not a newcomer can be trained by the Jedi (scientist)/have a potential to be successful.

Note that the projects evaluation happens on ScientificCoin not just by people with scientific background.

People with different background can participate. This allows to evaluate the project from various perspectives and achieve the best results.

ScientificCoin will have a social platform for all these people with traditional social media platforms features.

According to the information found in the ScientificCoin project videos on YouTube, there were near 120,000 users already on the platform in November, 2019 with 1000+ scientists/students with different scientific degrees.

Once the project gets evaluated by the crowd, it gets a second score. And the final score is determined based on these 2 scores.

This is how we get a rating for all the projects listed on [ScientificCoin crowdfunding platform].

You can click on the records in the table to see the details about every project including information about its creators, FAQs etc.

There were about 100 project as of time of writing. 11 of them passed experts evaluation.

The projects evaluated by the algorithm are highlighted in red, while the projects evaluated by experts are highlighted in green.

(image source)

Own tokens and smart contracts

With the help of ScientificCoin platform people can create their own tokens, smart contracts (no need to be an IT professional) based on the Ethereum blockchain (ScientificCoin team plans to create their own blockchain in the future), and begin to search for funds/investors. They can do so after the evaluation of their projects once they feel like they have enough feedback and followers [1].

Fundraising takes place in US dollars, Euros or other popular currency. In the presence of a smart contract, most popular cryptocurrencies can be used as a payment instrument. All funds go directly to the bank account belonging to the scientific project.

[source]

This process resembles me a little Steem SMTs (Smart Media Tokens) which will help people to create their own tokens to monetize their web-site and more.

Note that the Jedi Council is located in the Council Tower (analogy for the ScientificCoin crowdfunding platform).

And at the end we can have a successfully funded project (Anakin Skywalker / Healthmonitor).

2. Freelancing platform

Aside from raising funds for scientific projects, ScientificCoin can help with monetization of the skills provided by scientists.

The platform should be found here https://hireascientist.com

As I mentioned, to be the best a dApp also should have a good User experience (UX) and performance.

That’s where ScientificCoin platform has some problems.

Currently we just can’t get access to the freelancing platform.

It shows “Error code: SEC_ERROR_EXPIRED_CERTIFICATE”

As I mentioned, ScientificCoin is the work in progress.

So, I hope they will fix it soon.

I suspect that ScientificCoin Freelancing platform should be similar to ResearchGate

which serves as kind of social network for scientists and allows clients to hire qualified experts in any field [2].

As for our analogy with the “Star Wars” film, the Jedi movement originates from the Tython planet [3].

(image source)

There was a Jedi community on the planet.

Just like that, ScientificCoin provides a freelancing platform (Tython) for scientists.

3. Monsterbrain (educational platform)

Well, this is going to be sort of MOOC (Massive Open Online Courses) platform like edX, where tutors will provide educational materials for students. All of them will have a chance to get rewards in the form of SNcoin (ScientificCoin token).

MonsterBrain is an opportunity not only to become smarter, but also to earn on it.

(source)

At first, you’ll need to pass a questionnaire with free-form answers.

Go to https://scientificcoin.com/monsterbrain and click “Get free coin” button or scroll down and click “First forms” button. And they everything is pretty much intuitive.

In the quiz you’ll see mostly questions in the field of economics like

(image source (during questionnaire ))

After the analysis of your answers you’ll be given the corresponding training program.

What’s more,

You can win not only intellectual gifts in the form of training courses and subscriptions for weekly trainings from developers of the Technopark. The best guys can spend their holidays in the educational centers of Europe: England, Italy, France, Germany.

and

You can win interactive training from Doctors of all sorts of disciplines or even learn from them personally during a month!

(source)

Initiatives like MOOC provides us a chance to get education on our own schedule for free.

Well, I don’t know what is going to happen and what you’ll see once you get the results of the quiz.

I’m yet to pass it myself.

As for our analogy with the “Star Wars” film, Jedi like Luke Skywalker were initially trained outside of traditional schools (actually I’m not sure they existed in the context of the film) with other Jedi (tutors).

The team

The idea of ScientificCoin project came from the scientists from Siberia (Russia), which had difficulties with funding their own project one day.

All the team members are well-known scientists.

To get more information, visit http://scientificcoin.com/ (scroll down)

ScientificCoin is based in the heart of Silicon Valley. And

Scientific Coin Inc. is a parent company which has subsidiaries in Switzerland – an authorized cryptocurrency company, and Russia – the creator of the software, mathematical algorithms and other intellectual property.

(source)

And finally, Galactic Republic symbolizes ScientificCoin ecosystem

(image source.jpg))

I hope you liked the approach I used here to provide you information about ScientificCoin project (encoding information about it into the scenes of “Star Wars” trying to find similarities/analogies between them) which meets all the criteria (well, at this stage it meets almost all criteria. They need to solve some problems (and improve) their websites) I specified at the beginning of the post.

ScientificCoin is unique in that it not only gives us a chance to make the world around us better, but there was no ICO.

The project was funded by venture funds (and probably, founders/team members).

I assume that the absence of ICO could probably help the project to grow more organically and reduce the chance for some scams.

Feel free to share your thoughts on this.

In order to minimize the environmental impact related to the usage of the blockchain, ScientificCoin uses

Proof-of-research technology in our unique version. The extraction of Scientificcoin does not require a senseless waste of electricity. We will use the well-known technology https://boinc.berkeley.edu/ for reward for mining.

(source)

a proof-of-research scheme, which rewards miners who perform computations on the Berkeley Open Infrastructure for Network Computing (BOINC) [12]. The computation for the consensus protocol is used for scientific computations, so the energy is used for very meaningful purposes

(source)

According to the information found on the platform and in their Telegram group, the platform is currently in beta and the launch will be in 2020/once they have 1 million users and token holders.

For that to happen, they provide kind of bounty program for users, where you need to spread the word about the project and bring more users to it.

For more information about the bounty, read https://scientificcoin.io/account/bonus

Note that once you referred 10,000 users, you can get a $ 5,570 Health Monitor device for free [5].

Plus, if you found 20+ buyers of the device, then you could

get one Health Monitor device (or 10% of the commission from $ 5570 – device price) for every 10 devices supplied under the contract.

source

For more information, visit

https://scientificcoin.io/account/referrals

FAQs regarding the project can be found here

http://scientificcoin.com/faq

As it was mentioned at the beginning, ScientificCoin addresses only some of the problems of today’s science. Personally, I hope they will try to solve all the problems (including publishing and collaboration problems), and possibly it will evolve into something bigger with GitHub-like platform for scientists to collaborate and publishing mechanism with fair/adequate peer review process or even dExperiment.

I’ve tried to talk about all this in my post here

Blockchain-Based Scientific Ecosystem (dExperiment is coming). General overview

and would be great if ScientificCoin also tried to solve “lost” science/funds problem (“lost” because of language barrier).

And, finally, I'd like to call ScientificCoin the most realistic “game“, because it’s science which is closer to reality. You see, we have receptors which allow us to perceive the world around us.

(image source)

Scientific devices/tools help us to extend our capabilities and approach reality.

(image source)

And the good news is that this “game” is for everyone. Everyone can make a difference.

The more scientific knowledge we have, the more realistic point of view we have, which is a good thing, because it’ll help us to make more rational decisions and be more creative when it comes to problem solving.

Read more...

(Image was taken from PodMiners whitepaper)

In this post I’d like to discuss the impact PodMiners might have on our society.

Language teaching/preservation

Users at PodMiners can upload their content in different languages. Also PodMiners partnered with TranslateMe (organization which is going to try to translate the Internet by combining translation industry with blockchain technology and human power with computers). This partnership will potentially allow PodMiners content to be available on more than 6,500 languages. Thus, content created on PodMiners will serve as an incredibly useful material for language learners. What’s more, PodMiners will help to preserve languages. And it’s important to keep the language diversity because

To have a second language is to have a second soul

[source]

Being a part of the environment and our culture, languages shape the way we think [1].

Hence, to have a more flexible way of thinking, we need to learn different languages.

There’re more than 7,110 languages spoken across the world [2].

We're losing about one language a week, and by some estimates, half of the world's languages will be gone in the next hundred years.

[source]

Audio/video-records and their transcripts help us to preserve phonetic, lexicological and grammatical aspects of our languages.

Scientific knowledge promotion/distribution

In order to succeed in life, it’s important to be as close to reality as possible.

Jacque Fresco said once that it is information that is closer to reality.

It’s science which is the most reliable source of information.

Being a medium for free and independent communication to global audiences, podcasts might help with scientific knowledge distribution among human population.

According to the findings of the study done by MacKenzie et al, there were 952 science podcasts in English available between January and February 2018. The study showed that the total number of science podcast series grew linearly between 2004 and 2010, and exponentially between 2010 and 2018.

(image source)

It was found that the majority of science podcasts series (34%) were devoted to general science, i.e. that which focus on different scientific topics. The rest of them were devoted mostly to physics and astronomy (18%), and biology (14%) [3].

In the previous post devoted to educational potential of PodMiners I mentioned the study which showed that podcasts are helpful at educating inner-city African-American men about diabetes prevention [4].

Also there were a number of other investigations mentioned in that post showing that podcasts represent a great supplementary material for educational purposes.

Based on these observations we may conclude that podcasts (and PodMiners) might serve as a great way for science communication to the global audience.

To familiarize yourself with science podcasts examples, you can visit Science Podcast Database added to the study about science podcasts as a supplementary material.

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This contest is an attempt to promote scientific knowledge among community in a fun and interesting way with the help of molecules.

Some people like to travel around the world and tell others stories about what happens outside of our organisms/cells in other countries.

And with “Identify the molecule” contest you can try to travel inside our own organism/cells and cells of the organisms around us.

For more information about this contest read “Identify the molecule” league. Prize: knowledge + 5/10 XRP + 200/400 TMN post.

Prizes/bonuses:

The prize here is

1. knowledge

facts, information, and skills acquired through experience or education; the theoretical or practical understanding of a subject

[Oxford Dictionary of English, 3rd Edition, Oxford University Press, 2010]

That understanding of our own organism and organisms around us is the real prize in the case of this contest. No matter what happens (whether or not you get 5 XRP), you can win (can acquire the knowledge by investigating different sources of information, remembering and using it to your advantage in the future).

2. 5 XRP

3. 200 TMN

Aside from XRP I’d like to add TMN tokens.

For the uninitiated, TMN is the token of TranslateMe project (it’s about combining blockchain technology (NEO in this case) with translation industry).

The reason I’m going to add this token for the prize pool of this contest is not only because I have them, but because this contest is quite scientific, and TranslateMe project might help to solve the “lost” science problem.

For more on this you can read my post regarding TranslateMe (TranslateMe (or Decentralization meets Translation industry). Part 2. The “missing puzzle piece” of scientific ecosystem. General overview) (and other posts of that series).

For more information on crypto-bonuses for this league, please refer to “Identify the molecule” league. Prize: knowledge + 5/10 XRP + 200/400 TMN post.

Consider these tokens as a bonus.

Images and text are the clues for you to guess a riddle (the name of the molecule in this case).

Note that

a) even though this contest is called “Identify the molecule”,

-> molecule (singular)

sometimes it’s not just a molecule which is responsible for a specific function, but rather a complex of molecules.

Example:

cytochrome c oxidase (Complex IV)

is a large transmembrane protein complex… It is the last enzyme in the respiratory electron transport chain of cells located in the membrane.

source

b) some molecules/complexes have different names. For example, other names for cytochrome c oxidase (example above) are

Complex IV (mitochondrial electron transport). Cytochrome a3. Cytochrome aa3. Cytochrome oxidase. Warburg's respiratory enzyme.

source

Any of those names would be a valid entry.

c) Some almost identical molecules are grouped into classes / groups / families.

Example:

Helicases are divided into 6 groups. RecD and Dda molecules belong to helicases group (Superfamily 1 (SF1)). In this case you would need to guess only the name of the group –> Helicase/ Helicases.

d) Some proteins can have different forms – isoforms.

Example:

There’re trypsin 1 and trypsin 2. In this case you would need to guess only the general name – trypsin.

Important

In order to get TMN, you’ll need to have NEO-wallet and provide me your public NEO-address.

If you don’t have it yet, don’t worry, I published a post on how/where to get it (O3 wallet).

Note that NEO-addresses provided by exchanges will not work in this case (+ it's safer NOT to keep your funds on exchanges). It's highly recommended to get O3 wallet.

If there’re no winners on any stage, the prize will be distributed equally among all users who provided any guesses for molecules.

Rules

This contest lasts for 6 days.

Given that I don't see a comments section on Coil, I set up a Telegram group for this league, so that you could leave your reply with the guess there.

Leave your guess (1 guess only) in the Telegram group.

Don’t edit your comment/reply and don’t provide any evidence that your answer is correct.

The first user with the right answer is the winner.

I’ll provide the answer in the Telegram group.

Some of the clues have already been provided in the post.

Additional clues will be given in 2 days (on Monday, February 10, 2020, 20:00 ± 2 minutes UTC) (I’ll update this post).

And the rest of the clues will be provided in 2 more days (on Wednesday, February 12, 2020, 20:00 ± 2 minutes UTC) (I’ll update this post).

The reason is that some people might need less information to make conclusions that the others.

Additional clues will be added at the end of the “Riddle” section before the “Rules” section with “Edited” label.

The winner will be announced in that group (+ I'll publish a detailed review of the riddle after a while) on Friday, February 14, 2020, 20:00 ± 5 minutes UTC, so it's recommended to check that group on the 6th day.

I'll ask to provide me there your XPR-address.

I’ll transfer the tokens (XRP + TMN) (if the winner provides me his/her NEO-address) to the winner on that day (February 14) and add the transaction ID in the Telegram group.

I’m planning to run this contest every week.

So, you should expect to see the 2nd week’s riddle for January on Saturday, February 15, 2019, 20:00 ± 2 minutes UTC.

The riddle goes below.

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