COPE Encyclopedia of Cellular Communication By Dr Horst Ibelgaufts, M.Sc, Ph.D

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COPE is all about how body cells 'talk' to one another.

This 'CellSpeak' explains, among other things, what normal cells and cancer cells (in fact, all diseased cells) do, what the differences are and what they have in common, how normal cells turn malignant, how this process is regulated and may even be reversible, why some cancers metastasize and kill and others don't, why some treatments cure and others fail and why it's all so complicated. The work is for specialists and their students, but the use of this knowledge in medicine affects us all (watch a clinician's Eureka moment on COPE video). Below now is an explanation of all that 'CellSpeak' without jargon:

(This project will keep all funds raised)

Dr Horst Ibelgaufts introduces COPE

 

 

Dr Lawrence Afrin comments on his Eureka moment on COPE

 

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It's one small step from Facebook ...

Think of cell-to-cell communication in the body as the cellular counterpart of 'real life infospace' and let's deal with that first. On social media we talk (much!). We listen (less so!). We are in contact people that we might never meet in the physical world. We tell the truth, are no strangers to occasional white lies, or lie brazenly and think nothing of it. We say things normally BUT SOMETIMES WE YELL. We shout things out to everyone or only confer with friends. We are succinct or redundant. We spread good news, bad news, rumors, and gossip. We "re-post" messages of others. We bore a lot of people with endless repetitions, sometimes barely rephrased - until everyone stops listening.

We respond to messages with a hearty "Yes", a defiant "No", a lukewarm "Maybe", or just keep silent. We reduce contents to "likes" or "don't likes" (thumbs up/down) and tell everyone "what we are up to". We praise or bad-mouth others. We engage in cyber-bullying, which can even drive someone into suicide. We do long distance conferencing or short-distance round-table discussions. We design schemes to increase the visibility of our own postings and drown those of others. Have I forgotten something?

... to Cell Book

Just give your imagination free rein: the trillions of cells in our body essentially do what we also do! For each of the 'real life infospace' activities mentioned above there exists an appropriate analogue in cellspace. What we do with words, cells do with chemical messengers called hormones and cytokines. These messengers travel with the blood stream, sneak through spaces between cells, reach even the remotest cell in the 'tissue outback', and are found in all body fluids (even tears, saliva, or urine). Just see these messenger molecules as the equivalents of SMS or emails (or tweets). Cells receive such messages through 'receptors' on their surface. Receptors you can liken to cell phones or email accounts (with a little help from your service provider) or - old-fashioned - to satellite dish antennas.

Between all body cells there is an endless stream of several hundreds or more of such messages that are received, interpreted correctly and sometimes misinterpreted, acted upon, or just ignored. That is why I draw the analogy: "All cells are on CellBook" - the perfect cellular counterpart of our social media. There is only one big difference: a lot of information in cyberspace is expendable, but in cellspace nothing is superfluous.

From fish to mice and man, hormones and cytokines constitute the universal networking language between cells! Knowledge of the vocabulary, grammar, and syntax of "CellSpeak" allows scientists and clinicians to understand much of what healthy and diseased body cells do, how they do it, why they do it, and - most importantly - how to harness this know-how for our own benefits. Biomedical professionals exploit these insights, for example, to 'normalize' functions of diseased cells. The importance of all this 'CellSpeak' is illustrated best by the successful treatment of a variety of diseases and our ability to eradicate certain types of cancers.

Please let me explain briefly now, why I try to reach out to you and ask for your involvement.

What exactly is COPE and why is it unique?

COPE is short for "Cells & Cytokines Online Pathfinder Encyclopedia". It is the result of nearly 20 years of hand-curated knowledge collection, consolidation, and navigation. COPE is a unique online information resource for biomedical professionals and their students with 45,000+ web pages covering 'CellSpeak’ and a lot of related subject matter needed to understand how body cells communicate and 'what they are up to'. One reason is the huge extent of its general content. One can make a lot of relevant information 'look upable' on 45,000 web pages enriched by more than 100.000 cited scientific references.

Why do I ask for your support?

For nearly 20 years COPE was an open access educational and research resource. Biomedical professionals, physicians and clinicians, and their students worldwide are making heavy use of COPE (ca. 4,000 visits/day in 2015). For the good of all, I am very much interested in maintaining the continuity of this work and possibly expand the contents of COPE for the biomedical community, especially for the students who will be the researchers, physicians, and clinicians of tomorrow.

During the past 20 years I personally shouldered the bulk of all costs connected with writing and maintaining COPE. I operate on a small local income from a developing country where I teach medical students. My limited means together with the increasing amount of work necessary to keep this resource going and up-to-date now make it impossible to keep COPE afloat without help from outside.

Sad to say, but most of COPE’s visitors are scientists and students who are themselves scrimping by with very little funding of their own and either could not personally afford, or did not have the institutional mechanisms to contribute the support I now need to keep COPE afloat. I have tried to solicit scientific organizations, academic and commercial, without success. I even tried installing a subscription mode but again had very limited success.

How much?

Sounds blunt? But, fair enough, that really is the cardinal question,isn't it? Well, the relatively low cost of living where I live means that just US$ 19,000/year (13.100 GBP; 16.700 Euros) would enable me to continue my work for one year and provide invaluable service to the biomedical community.

How would I use your funds?

I'll make use of your generosity as follows:

- $7,000 (4.800 GBP; 6.200 Euros): programming costs;

- $2,000 (1.400 GBP; 1.800 Euros): computer and some software;

- $1,000 (700 GBP; 900 Euros): print journal subscriptions

- $1,000 (700 GBP; 900 Euros): local internet connection,

- $8,000 (5.500 GBP; 7.000 Euros): author's salary.

What's the reward?

Your and my reward? Your generosity would allow me to abandon the subscription thumbscrew for COPE and go back to open access for the good of all. Your help now would benefit thousands of biomedical specialists and their students, who are the physicians, clinicians, and scientists of tomorrow. Living in a developing country has taught me like nothing else what 'restrictions and limitations' really mean and how they affects lives. Free access to COPE is, I believe, a model in which visiting researchers and students are most likely to find the information that might give them their next great insight or idea in research and in clinical use – but it is not a model which, by itself, will sustain my own efforts. Just take a quick glance around COPE: I am positive that you’ll agree it must take a lot of commitment and effort to maintain a resource like this. I can offer more cartoons. Sounds weird, I know, but what else can a lexicographer-cum-artist living in a remote corner of the world offer? I have never done a webinar, but, ahem, I think I am a good story teller. But that would require a new computer (I can't even run Skype) and a reliable internet connection. I can also acknowledge top backers on my website - unless you want to remain anonymous.

The bleak alternative?

Well, that is to shut down COPE. Personally, this would sadden me, as you may imagine. For all users of COPE it would mean what some users have called a "tragic if not catastrophic loss" of 20 years of knowledge consolidation - a very important aspect of biomedical informatics, the significance of which is ever so often overlooked in the race to create more and more 'new' data.

Shutting down COPE would mean the loss of a vast body of detailed and important medical knowledge. Be that as it may, I hope I have succeeded to convince you that my project merits your attention and is worthy of your support. I hope that you realize that, if COPE disappears, it is very unlikely that someone else with enough experience as a lexicographer, dedication, and the scientific background will come up with a similar resource with the same extensive and cross-referenced coverage of COPE. Maybe you understand then why I say "please help me to fend off bleakness".

Where do I get more information about COPE?

Register at www.cells-talk.com for a free trial period to explore COPE contents. I am confident you won’t have to explore for very long before realizing the value that COPE offers to anybody trying to understand human biology and disease. http://www.cells-talk.com/index.php/page/whycope contains a selection of testimonials / credentials. Please read there also about the 'Eureka moment' Lawrence Afrin, MD, had on COPE. The insights gained benefit many patients already, which pleases me no end.

May the force be with your cells!

Thank you very much indeed for your patience in reading this. If you can give this project your "likes", please alert your friends and followers about COPE for posting and reposting. Your support will help thousands of scientists and students all over the world every day. Who knows what great biomedical development tomorrow will be a result of your generosity for COPE today?

You can reach me at cytokines@copewithcytokines.org.

With a friendly smile, sincerely and cytokineologically yours,

Dr Horst Ibelgaufts

 

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I have been consolidating information pertaining to cellular communication for the past 20 years. This project has turned out to be of great help to biomedical professionals, including cell biologists, immunologists, endocrinologists, oncologists, hematologists, virologists, molecular biologists, physicians, clinicians, and their students. Practically everyone in the highly complex world of communication biology uses COPE – from research scientists to product managers in academia and industry. Apart from my personal interest in the subject matter, this is reason enough to continue.

The COPE Encyclopedia is unique because it is the only existing resource that puts the focus on highlighting the manifold interactions between cells and the messages they exchange by using hormones and hormone-like proteins called cytokines. These relationships provide the value-added information urgently needed to understand cell and organ functions and the manifold connections between organs. COPE puts all information into perspective by embedding the plethora of specialized facts in a vast amount of more general subjects needed to understand critical information in context.

Some clinicians have told me that a discontinuation of this project would be "a catastrophic loss", especially as it is highly unlikely that someone else would ever come up with a similar resource that covers communication biology right from its inception to present day.

I operate on a small local income from a developing country, teaching medical students.

My limited means now make it impossible to keep COPE afloat without help from outside. I have had little success with soliciting the help of scientific organizations or with the creation of a subscriber-only version of COPE to improve the funding situation. The only remaining option therefore is crowd-funding.

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Why is COPE important for cancer research and biomedicine?

There is a very intensive cross-talk between normal cells and cancer cells, and this has a tremendous influence on both cell types. One cannot understand one without the other.

The actions of the communication molecules described in COPE can promote or block, among other things, the differentiation, the growth, or even the death of normal cells and cancer cells. They explain also, for example, how cancer cells evade the immune system, how they usurp normal body functions (e.g., processes leading to wound healing or the growth of blood vessels) to secure their own blood supply, and how they can metastasize to different distant regions of the body.

Without a detailed knowledge of these complex processes it is virtually impossible nowadays to make meaningful statements or predictions of the behavior of normal and cancer cells, to understand why conventional cancer regimens work (or don't), let alone to develop new treatments. In one way or other the information collected in COPE entries directly or indirectly also promotes:

• the causal understanding of the nature of normal and cancer cells

• a more 'holistic' view of disease through the focus on the relationship between individual cell types and entire organ systems, for example, the liver, muscles, or even body fat, which are seen now as hormone-secreting collectives influencing one another's activities

• the realization that mind and psyche can also influence cellular communication and 'talk' between such collectives – which already resulted in the discipline known as psychoneuroimmunology. One can also easily envision the development of some kind of psychoneuroimmuno-oncology.

 

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Horst Ibelgaufts is a molecular biologist who studied biology at the University of Cologne, where he earned his Master's Degree. His PhD thesis at the same university (Institute of Genetics, Max Planck Institute for Brain Research) was about virus-induced brain tumours. He spent some postdoctoral time at the Institute of Animal Genetics, University of Edinburgh. After that he was at the University of Munich (Institute of Biochemistry and Gene Center) and then emigrated to a developing world country, where he teaches medical students.

Horst Ibelgaufts authored two quite successful books, a Dictionary of Genetic Engineering (in German), and a Dictionary of Cytokines. Apart from that he wrote some non-fiction under a pen name.

 

Hello! My name is Horst Ibelgaufts. I am a molecular biologist who - single-handedly – has been writing the COPE Encyclopedia of Communication Biology (www.cells-talk.com) for the past 20 years. I ask for your support because insufficient funding is now threatening to snuff out of existence this unique resource, which has provided great insights for researchers and clinicians worldwide and has potential to continue doing so for many years to come.

About my history as a "dictionary maker"

My first dictionary I compiled as a teenager when a neighbour who was a teacher left me with about 5 meters of old Reader's Digest. We had no space so I tore out all articles that somehow interested me and was faced with the problem of creating some kind of index for the many folders of articles. I numbered the articles, assigned "entry terms" under which I thought I might want to find the contents, and created a hand-written dictionary: all entry terms in alphabetical order with a cross-reference to the article number. Practically an index to a general knowledge treasure trove. I learned a lot about "cross-connections" and "connecting the dots" even if I was not aware of this.

At the University of Munich I translated/updated the first Textbook of Genetic Engineering written by our head of department. During this work I realized that a textbook, nice and useful as it may be, is very different from a dictionary. Textbooks enforce linear reading, but that is not what people usually do. Frequently, the first thing a reader does is to look up a term in the index - a dictionary in itself where the entry content is just page numbers - going to that page and hope that what one finds there is sufficient. I convinced the publishers that what was really needed was a Dictionary of Genetic Engineering where people can look up thngs by keywords. During this work I decided that simple one-liners are not enough and to be of use for students the entries should be selfcontained, have cross-references to other entries. As an example let me give you the term "Southern blotting". The definition in a pocket dictionary I found was something like "technique for transferring nucleic acids from resolving gels to filter membranes for further analysis". Utterly useless in its brevity, making sense only to those who already know what the term means. So I decided that my Southern Blot entry should describe what the technique is about, how it is done (without the lab cookbook details), how the data obtained looks like, what they tell you and what they don't tell you and what other methods are available to obtain further information. I saw the dictionary as a vade mecum . I carried this concept through when - in response to success of the Dictionary of Genetic Engineering - I agreed to write a short Dictionary of Cytokines in German for a local publisher. At that time I did not even know what Cytokines were. Unlike what one might think, having no knowledge about a subject and then write a dictionary is probably the best and most suitable starting point. Unlike "specialists" in the field who often are so engrossed in the subject that they have forgotten how it feels to be a struggling newcomer and how much is simply taken for granted when reading scientific articles, a newcomer knows well what he knows and does not know, what he understands and what he does not. In a way one has a keen perception of what should be "look upable". This attitude resembles that of a science journalist who writes for a general audience and is tasked to take little for granted.

From the German Dictionary to an English updated edition (with a different publisher) was only a small step. During this work I also developed a keen sense of "cross-connections" and crossreferences and had the idea that html pages were just the ideal medium for such a dictionary. Not having programming knowledge, I asked my brother Jürgen, who is a programmer, if he could not develop a programme that would read ana analyse my source text (word processor), create an html page for each entry, and then create crossreferences between all entries. The first programme written in COBOL, took about 18 hours to do this when the dictionary only had about 2000 entries. He later rewrote the programme and now I can have a dictionary of about 45.000 entries completed as hypertexted web pages in less than 6 minutes.

The topic of connectedness fascinates me and is expecially appropriate for such a complex field like communication biology with its thousands of chemical messengers, hundreds of cells, and umpteen clinical conditions, including hundreds of different types of cancer cells. I have used this dictionary-generating programme privately to create two language dictionaries (Hiligaynon to English, Tagalog to English). During this work it occurred to me that this cross-referencing concept can be carried a step further. I came across the question of what to do if one only has access to a unidirectional dictionary (Hiligaynon to English). Even if one knows, for example, that kayumanggi means brown, there is no way to look up, for example, what the colour red is in the other language. So, in my language dictionary, I began to add related terms for all entries. Thus, one can travel from "kayumanggi" to the word "duag" (the word for colour), and there one would find a complete list of other colours. Apply this principle to practically every entry term, and you get a very useful knowledge base that makes it easy to pave your own pathway between individual knowledge islands, streamlined and adapted to your own pre-knowledge of a given subject matter'

 

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Hello, it is me again - and only with a pharmacologically insignificant dose of "science" sprinkled in.

The purpose of this page is actually to introduce a video of a different kind, but being a rather talkative person, let me just lead you up to this slowly and also show you a little bit of the real person behind COPE.

It may have crossed your mind that someone who collects and consolidates very specialised knowledge and sticks with a project over 20 years without getting terribly bored is somewhat of a rarity nowadays - if not a downright oddity. After all, modern life seems to go with attention span disorders and reduced staying power. I seem to be surrounded by growing numbers of people who have difficulties with handling text exceeding twitter limits and become fidgety with video clips longer than 30 seconds.

Let me be odd then and add another smattering of eccentricity to the person behind COPE. It takes all kinds of people to make a world.

First of all: don't look so astonished. I am doing exactly what you think it looks like! I am indeed pumping water from the well!  Much to the delight of the grocery store owner here, I use lots of black tea while COPEing and get quite a bit of exercise through pumping. My physique shows that it does not seem to help much but I have decided not to worry about my adipose tissues, their cytokines (called adipokines, by the way), and the abominable body mass index.

But just to make sure you'll get my point: there is no running water here and the most reliable source of hot water is the gas stove. I spare you the details of "brown-outing" electricity, which, if nothing else, teaches me that the battery on my museum piece of a MacBook Pro is what one can call with a lot of goodwill: "achievementally compromised".

The second image gives you an impression of where I live. Looks idyllic, does it not? Good place to think and read and work with little distraction! Always the danger, of course, of freely falling coconuts when you work outside. But so far my laptop and I have been quite lucky indeed. Only had a single near miss encounter so far :-)

And then, of course, there is the nearby beach where I live. Not the kind of smooth sand beach that people want. Very stony! Very slippery mudstone. Just lovely!

Thank Goodness for that because the big advantage is that the beach can't be "developed" - which, sad to say, more often than not simply means ruined! And I get more exercise with my daily walks along the beach, picking up coloured pebbles. And these I can use again for educational "artwork", spreading wise thoughts.

I employ a cell phone as a wifi router, IF there is a signal. Why there is no telephone landline with internet in my place is too long a story to tell and does not really make local providers look good. Be that as it may, each day here reminds me of the NET part of the word internet. A net, when you think of it, is mostly nothing at all, isn't it? I mean, mostly holes (a German poet in the 1920, if I remember correctly, once called holes a "positive manifestation of a negative totality!). Well, do you get my meaning? Yes, what people call connectivity is certainly different here.

I am determined and dedicated enough to slog on, even under these conditions. Referring to my dictionary work some friendly soul recently told me "It is often this dedication that makes the seemingly impossible happen in Science."  I would never have put it this way, of course. I am just enthusiastic about my dictionary work - and without interest and enthusiasm I could not have done 20 years of COPEing. And I really do pity everyone who is forced to do work without enthusiasm or - worse - lost it over the years. Oh well ....

But, as I said at the beginning, what I really wanted to show you on this page is the video. Just can't help being playful when I am not COPEing, and never stopped dreaming.

Sorry if the text in the video sounds all quite involved for a lay person - the typical jargon of biomedical scientists. Jargon is just inevitable in any profession, and I hasten to add that we don't use jargon to impress people. To tell you the truth, I used this piece as a new year's greeting card for some fellow scientists some time ago.

By the way, one of the aims of COPE - most decidedly - is to knock at least some holes into existing (jargon) language barriers between and among different scientific disciplines. And believe me, I cannot think of another discipline that is as multidisciplinary as cellular communication biology. The whole discipline is a zoo of factors in a jungle of interactions surrounded by deep morasses of acronyms and bleak deserts of synonyms all doing their bit in many different ways to make it difficult to get to the sleeping beauty.

The aim of COPE is to straighten things out, to function as a vade mecum in the old-fashioned sense, and to prepare newcomers and specialists alike for the real dogfight with the specialised scientific literature.

Behold and despair, dear reader, with one of the semantic masterpieces I encountered many years ago when working on COPE: "In contrast to BCDF-gamma and BCDF-epsilon activities of BSF-1, BCGF-2 could function as BCDF-alpha." Can things get more cryptic than this? I assure you: they can get more cryptic.

I could explain everything, of course, over a cuppa tea. No! Don't even think of Skype. It is not an option: Microsoft scoffs at my old operating system, and even if it did not, internet speed here is quite often complacently unspeedy and sometimes octagenarian pedestrian. Hm you could send me an old-fashioned email, of course, but for the time being just enjoy the music then, and tell me if you did. :-)

You may share the video, if you like, and tell others to do the same.

And, ahem, please DO consider a donation to keep me and COPE afloat and tell your friends to do the same.

Who knows, I might even come up with more of this kind. The music is there already, having a young composer in the family. Only the words I still have to think about. And as you know, the devil is always in the details, especially with words. :-)

Well then. Be kind to your cells, don't overwork your cytokines, and enjoy your day.

Horst Ibelgaufts

 

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Howard Young
COPE is truly a unique resource that should be of value to everyone who has to think about cytokines with respect to their research. This incredible effort by one individual deserves support from the research community. I urge my fellow scientists to think of the global community and support this resource. Howard Young
31/10/2016 17:27:59
David Alexander
My fellow Americans have recently made the disastrous decision to elect Donald Trump as their president. The users of COPE are currently making the decision to close down COPE. Without user funding, Dr. Ibelgaufts will not be able to maintain COPE and this amazing website will be gone. So, to all users of COPE, please ask yourself if COPE is worth the price of a dinner for two. David Alexander
27/01/2017 14:27:54
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