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Posts Tagged ‘Science’

Why publishers?

This year I participated in organization of a computer science conference. To my surprise, I found that conferences hire publishers instead of publishers own the conferences. Here is how organization of a usual CS conference works.

A conference is defined by its steering committee, which is a small group of top academics from the field of the conference. The steering committee appoints program chairs every year. The program chairs of a year sign a contract with a publisher to publish the conference proceedings. These contracts are signed every year. The program chairs organize the conference independently of the publishers.  They appoint the program committee with the approval of steering committee. The program committee reviews the submitted papers and accepts a subset of the papers. The program chairs send these accepted papers to the publisher for final printing. The copyright of the papers are held by the publisher in return of providing the publishing service for free.  They also give some free copies of published books to the program chairs. The copyright allows them to charge exuberant amount of money to the academic institutions to access the publications.

The natural question comes to mind: “Why publishers exist?”.

One may argue the following three contributions of the publishers.

  1. Quality Publishing: The publishers proof read the papers. Sometimes they  move around figures to pretty-up the paper. This task is usually done by some third party company located in some third-world country. They assign ISBN number etc to give the proceedings a unique identifier. And finally, they publish the physical books. Publishers do not make any editorial decisions.
  2. Reliable Dissemination: These proceedings are usually available at the publishers website for rest of the eternity. For Academic libraries, it is easy to follow these publishers to find most of the scientific literature. Publishers make dissemination of scientific works easy.
  3. Legacy Reputation: If publisher signs publishing contracts  only with high quality conferences then they build a reputation over time. There are no lack of conferences in academia. Academics keep inventing conferences to promote themselves. But if the proceedings of a conference is published by a publisher then the conference inherits the reputation of the publisher.

The first two contribution are already obsolete. The proof-reading service can be provided without the publisher. Usually, the cost of doing research is very high and hiring a proof-reader should only be marginal. An institution can easily pay for proof-reading of its papers by those third world companies. The printing of physical books and hosting the papers on internet are fast becoming inexpensive technology.  The cost of running a scientific publication website can easily be covered by scientific funding agencies. Anyway, they are paying for producing the content. Why not they also pay for dissemination?

The reputation of a publisher is the only reason, I think, that keeps them in business. While evaluating a published work, funding agencies factor in reputation of the publisher. This makes life of evaluators easy. Therefore, the steering committees of the  conferences do not want to move away from reputed publishers. This is hardly a compelling reason to have publishers. This is a classic legacy systems problem.

The underlying technology for publishing scientific works has shifted sufficiently that makes “the publishers” irrelevant and unnecessary overhead. All the scientists I have spoken to also say that they do not see any value of having publishers. However, it is very hard to chart a path from current system to a publisher-free system, without breaking scientific reputation system. Here is a great opportunity for innovations. I am very sure soon scientists will start experimenting with different publishing models for important conferences.

Book: The lac operon — How do we know what we know?

I read The lac operon, which is a book about the history of the scientific work that led to our understanding of the DNA mechanisms that regulate the cell activities. The title ‘lac operon’ is from the name of a DNA mechanism that regulates lactose ‘eating’ in E. coli bacterium. The lac operon was one of the first examples that were analyzed.

The book is not so well written. The narration in the book is convoluted with the experiments and some anecdotes about the scientists behind those experiments. Very often these anecdotes pop up suddenly and break the flow of some scientific argument and vice versa. This book has great content but needs a good story teller like the author of Logicomix.

One anecdote caught my attention.  According to the anecdote, 50th birth day of Francis Crick was celebrated by presenting him a naked woman at a scientific conference! (You can find it at the end of the top paragraph of the page in this link). Even if it was not a real one (not clear from the text), it is outrageous. Was there no woman in the conference? Well it was still 60’s. Perhaps in those days, you could do such things without being called sexist and thrown out of scientific community.

Limits of decision making!

Here is very interesting letter from Kurt Gödel to Von Neumann. In the letter, Godel says that if we have fast enough computer which checks, within few days, that if a proof of a mathematical theorem can be written in few hundred pages then only it is worth trying for humans to look into the problem. Otherwise, proof will be so long such that it is impossible for human mind to find the proof. If such computer can exist then all the creativity expected from a mathematician is to ask computer to prove a right theorem. So far, we haven’t developed such computers. So, we have to rely upon human creativity to find a proof for a theorem.

Implications of above statement are much wider. Finding a proof of a mathematical theorem is strongly related to difficult decision-making process in ordinary life. We face such difficult problems also in our ordinary lives. For example, you have 2 job offers and you have to choose one. Lets see how you might evaluate that which job is better for you. You will consider the amount of salary. You will also consider how the pay will change over the years. This follows that you need to evaluate the company under many criteria. You need to evaluate the work environment of the company, kind of career paths you would like to take in the company, stability of the company, flexibility of the company in future market conditions. This list can go on and on and on. You may get overwhelm with the difficulty in choosing the better job. This example suggest that there can be following problems in evaluating these criteria.

  1. You may have too many criteria to evaluate. ( Large problem )
  2. You may have too much data to process for some criterion. ( Large Input )
  3. You may not have enough information to evaluate some criterion. ( Insufficient information )
  4. You may not know how to evaluate using the data. ( Undecidable )
  5. You may know how to evaluate the criterion but it takes too long to evaluate. ( High Complexity.)

Above problems limit our decision making capacity. So, you are faced with the similar problems as mathematicians. Mathematicians can choose not to prove the theorem and attack some other problem but you have to pick a job, you have to pick a spouse, or you have to pick a health insurance. Life presents you situations in which you have to make a decision with limited resources and well reasoned decision is just impossible in limited resources.

Above observation shows that reasoning and logic is insufficient to live ordinary human life. There you need wisdom. In difficult situation, people follow the known wisdom of the society, follow advice of elders, or just-do-something-and-see-what-happens. It is one of the reasons why we have prevailing superstitious believes in our societies. Superstition have this positive aspect then there are huge drawbacks. People tend to drawn into ease of superstitions. They don’t want to analyze or may not be aware that matters life can be analyzed. This leads to highly dogmatic society. Once society takes a bad decision then it continues for centuries. Even if in future due to learned experience and analysis, it becomes possible to show that traditional wisdom is a bad decision, people resist too hard to change their life.

In last 300+ years of industrialization, thinkers have observed that we have been using too much wisdom compare to logic. Many questions of life can be decided using logic and we simply depend upon traditions and wisdom. So, there has been a grand shift of paradigm in thought process in which people have been applying more and more logic and reasoning in ordinary life. We have seen in the past there have been philosophical ( Rene Descartes, Friedrich Nietzsche) and political (Ayn Rand) movements which says that logic and reasoning is the only guide line of human life and all the traditions which can’t be demonstrated via logic should be abandoned or at least questioned. These movements have gained significant support time to time but lost their appeal to people soon. People find that logic can’t answer all of their problems. There are limits as we have seen at the start of this post.

We see more clear evidence of the difficulty of decision making in public policy debates. For example, health care debate in US. US government has been trying to design a health care system which is most fair and effective. The system will run over 300 Million Americans which will be eventually highly complicated. No one can logically demonstrate that some health care system is the best effective choice. At the end, you see in public debate in which people are arguing over different conclusions which they didn’t logically deduce but concluded using their wisdom. The debate soon reduce to a cock-fight.

We need to build a culture which tries to apply as much logic as possible and when logic is unhelpful then we can depend on a good set of wisdom, which is passed from one generation to another generation.

Science, Scientist, and The People!!

September 13, 2009 Leave a comment

Science is objective. Therefore, it has more predictive capacity of material world than common sense. Therefore, it is useful. Therefore, people has to pay attention to it. Therefore, society has to pay its bills. Science can be very useful tool for the society but if society doesn’t understand its nature then it can be totally ineffective tool. As it has become ineffective in environmental change debate.

The essential nature of science

Science is not so straightforward in practice. To gain a scientific knowledge, one has to go through following 3 challenges. Who is observing the objective reality?, How is the objective reality observed?, and What is concluded about the objective reality?

1. Who?

The objective reality can not manifest itself without an observer. A scientist along with some instruments is needed to observe the reality.  The integrity of the scientist and his instruments have to be assumed otherwise the reported observations have no value in scientific sense. This integrity can’t be fully verified. Moreover, one can say that it is impossible to fully verify the integrity of the scientist and his instruments.

2. How?

If a scientist embarks upon observing an objective reality then she has to make many decisions. She decides which experiments to conduct, which instruments to use, and which information about the objective reality to collect. The selected choices heavily depend on the personality of the scientist. The difficulty is that all objective realities depend upon infinitely many factors. No matter how carefully the scientist design the experiments, it can’t take all those factors into account. So, it is impossible to fully observe the objective reality under investigation.

3. What?

After collecting those information about the objective reality. One has to make sense out of the information. At the final step, scientist has to supply considerably concise theory about the objective reality there is. For a given amount of information, there can be multiple explanation of the same objective reality. The scientist picks one explanation which makes most sense to her and reports it. So, it is quite likely that the produced explanation is not entirely correct.

How do in practice scientists deal with above 3 steps or 3 problem?

As we saw above that each of the 3 steps entails a kind of impossibility in achieving the desired goal. Following are the means using which  scientist deal with each of the problem.

1. Who?– Respect in the Community & Redundancy

It is fair assumption that if the scientist has high integrity then she will use the instrument with high integrity. One individual can’t deal with such a high standards of personal integrity all the time. It is human nature to get easily seduced to lose one’s integrity. Therefore, scientific work is done in the form of communities. For each distinguishable subject matter, e.g. Physics and Biology, communities are formed.  The individuals who belongs to the community observe an objective reality and report it back into the community. These reports are read by the community members and they critically assess the integrity of the report, i.e., assessing integrity of the observer. More often someone reports trustworthy facts, one becomes more respected. Meanwhile, other individuals of the community try to observe the same objective reality. This redundant work may verify the previous observations or some times they may show that previous work had mistakes. In result, we learn a set of observations which are correct ‘beyond reasonable doubt‘.

2. How?– Standardization

The community of scientist soon face the problem of the second step. They slowly achieve consensus among themselves that what and how much should be observed to gain confidence on collected observations. This standardized procedure is commonly referred as the accurate methodology of experiments. They refuse to accept reports which doesn’t comply with this minimum standard of methodology of experiments. Notice that this standardization of the observation procedure is not done by an individual but by some set of individuals. In result, we use a methodology which is useful ‘beyond reasonable doubt’.

3. What?– Regress and endless discussions

Scientist carefully examine collected data and propose the potential theories to explain the reality. They debate endlessly about these theories. They refute most of the proposed theories in their course of discussion eventually they left with few contending theories. This provoke more need of collecting observations such that we can conclude at the final theory and refute other contending theories. As these new observations come in, more mysteries unfold and more discussions provoked. This process is summarized by the philosopher Hegel as Thesis, Anti-thesis, and synthesis (Dialectic). Observe that this can be endless process or may take very long time to synthesize the final theory. So at any movement of time, we have a set of potential theories which explains the reality ‘beyond reasonable doubt’.

Perception of science in society

People in general are indifferent with how scientists work. They have seen significant benefit came out of scientific investigations therefore it is not a bad idea to pay for scientists. The problem comes on the surface when society demands actual advice on matters of the science. People in general demand definite answer from scientists with complete certainly. As we have observed, the scientist can only respond with a theory beyond reasonable doubt.

For example, people regularly go to Doctors and get advice for their health. A doctor can only tell his patient that if he takes this medicine then he may potentially get better. Unfortunately, most people take their doctor’s word as a word of certainly. If the patient doesn’t get better than he only curses the doctor and goes to another one.

Environmental change debate

People some times demand advice from scientists for public policies. Such as, up coming environmental disaster. People want to know how the environment is changing. How bad is the impact of human activity? How much time is left before this environmental change can’t be reversed? Is there any problem at all?

If really there is upcoming environmental disaster then people have to act collectively. This has triggered a great debate of environmental change. People ask scientist to come up with an advice. Some individual scientists produce articles which describes a potential theory which says that there are global events in environment which indicate significant change in Eco system of Earth.  The articles also suggest to control emission of green house gases, reduce exploitation of natural resources, and protect wild life.

Some powerful people don’t like their suggestion. These suggestion may change the public policies which might take away fortune of these powerful people(owner ship of coal mines, forest land, or low production of oil). They start a reverse campaign against those scientists. They say the proposed theories are not full and final. These theories are simply potential theories. They conclude that these theories have no more value than personal opinion of the scientist who is writing them.

As scientists observe this move in the debate. They say that our theories has more value  than opinion. The scientific community comes together and publish a common statement about the theory they believe in. As we have discussed before that a proposed theory has to be accepted by the scientific community at large to become a scientific theory(or a theory beyond reasonable doubt).

In public eye, this appears to be a political action taken by the scientist. These statements are dismissed on the ground that scientific truth can only be stated by a single person not a community.

In result, voice of scientist is lost in this squabble over who? how? what? is trustworthy.

Why are Creationists winning the battles?

January 14, 2008 Leave a comment

Here is a YouTube video which shows the argumentation between a creationist and a evolutionist.

Creationist’s position is very safe in a setting of debate. There are very limited ways to disprove them. They build their theory on top of some set of holy scriptures. One can disprove them by finding a contradiction within those scriptures. Other way to disprove them is to find a wrong natural fact stated in the scriptures. A creationist doesn’t have to show any evidence for his theory. Absence of an alternative explanation makes him right.

Creationists had observed problems with their theory long before scientific methods can notice. They have developed detailed list of escape routes from the attack of science. If you think naively that I understand science so i can easily refute creationist claims then you haven’t engaged with creationists. They know better about science then you would know about religion. Creationist’s objective of debate is not to find a right answer but to make sure that arguments of the other side don’t reach to the audience. During the debate if scientist doesn’t see this happening, she will certainly fail to make a point.

How does creationist escape?

Holy scriptures has been a dominating source of knowledge for a quite long time. You are not the first person who is examining them critically. In medieval times, there has been lots of effort to re-interpret holy scriptures again and again as any reasonable objection had risen. There has been mutually contradictory interpretations of the same scripture at different times by different people. In essence, they fix some set of holy scriptures and try to come up with a sane interpretation. This whole interpretation business has evolved in last 2000 years such that all possible inconsistencies can be removed. It is not the case they have removed all of them. It will be very hard to find an inconsistency in holy scriptures which can’t be fixed by a little twist of interpretation of the holy scriptures.

One can also try to find a wrong claim about a natural fact in holy scriptures. Creationists have already prepared its answer. All the holy scriptures are written in poetry. So, it is hard to decide that which part of the scriptures is direct description or which part is metaphorical. Again, this freedom of choice is subject to ones interpretation. Creationist will say that scriptures are not wrong but the interpretation is wrong.

Why does scientist fail to win the battle?

Creationist use people’s week understanding of scientific methods as their main tool. He just want to show common people that science is not the answer of all their questions and problems. Science is incomplete. It doesn’t answer everything. He will push scientist to the point where she can’t answer any further. At this point, she has to say I don’t know. Creationist will catch up right at this point and provide religious explanation. He can always do it because religion explains everything.

Science depends on experimental data. If an hypothesis is supported by enough data then it becomes a theory. Creationist will ask scientist what if all of your data is wrong. An honest scientist will say that it is quite possible. Creationist will immediately claim, “See! these scientists are not sure of their own theory. So, How can we believe them?”

All human knowledge, including science, is axiomatic. Creationist will show you that religion has axioms. Science also has axioms. Hence both are same. No one has an advantage over another. At this point of argument scientist feels lost. She doesn’t want to actually say the right answer to creationist’s claim because the difference between scientific axioms and religious axioms is subtle.* If she tries to explain then people may not listen.

The essence of science and its power can’t be explained in an hour long debate. Someone has to spend time and learn the ideas of science. Only after spending some time one can make sense of it.

How to do science?(2)

October 30, 2007 Leave a comment

“A talk is advertisement of your work. A good presentation is full of little lies!”

[ Here, my objection is not an argument but an opinion. ]
Presentations should be fluent, simple and clear. One should try to make them as easy to understand as possible. One shouldn’t throw many ideas on listeners face. One should try to use as simple language as possible. It is hard to follow these guidelines even if you know them.

But, I am against this “Advertisement” view of scientific presentations. Science in essence boring and it excites only boring people. Science is attractive only to a person who likes flow or reason across arguments. Packaging science in superficial exciting look doesn’t help science anyway. This can only attract people who don’t appreciate the rude and sharp nature of science. I have a feeling that there is a certain percentage of PhD students who do not really understand essence of science. They undermine the process of scientific reasoning.* Someone said that,

“Things should be made simple but not simpler!”

There is no science for layman. Either you understand it or you don’t. There is no simple explanation of complex ideas. An idea should be presented simply only if it can be simply presented without loosing soundness.

“A good presentation is full of little lies!”
This act of pretension, hand-waving can only mislead people. I hate when i see people doing this in their presentations. Some times these ones are considered the best.

It is presenter’s choice how he wants to do it. I will not say some presentation is bad until I understand what is presented. No matter how boring or flashy way it is done. If advice like above are advocated then i will stand to reject it.

* I don’t claim that i understand best about science. I am in process of learning and this is an attempt to tell what i think. Feel free to counter my opinion as blatantly as possible. 🙂

Categories: Science Tags: ,

How to do science?

October 19, 2007 Leave a comment

This summer i did a course about, “how to do research in computer science?” offered by a great prof. It gave me a good overview about how scientific community in computer science behave. I learned many good things in the course but some things seems directly contradicts with the basics of science. One of them is:

“Cite others respectfully. Don’t reject others ideas in flat words. Otherwise you will make bad relations with co-researchers.”

My objection:

Science has three specific objectives for crediting somebody for discovering some knowledge.

a) To motivate people to do more and quality research such that they can become famous.

b) Nobody has tested all the scientific knowledge by oneself. We just assume many facts. In this way of dealing with knowledge, It is quite possible that some wrong mythical facts creep in as scientific knowledge. If we hold responsible somebody for each fact then this effect can be avoided. Whenever, someone wants to write a book on some subject then one can directly go to the experts of the subject and hold their neck for their claims. If the founder of the particular fact is already dead than well indexed papers can be used to authenticate. If in future some one shows that a paper has a wrong fact then this paper can be tagged for being wrong. In essence, credit system provide a bug prevention mechanism.

c) This credit system keeps the history and chronological order of discovery of knowledge. By studying evolution of science a researcher can learn how it has been done and what excited the earlier scientists. It can provide intuition of scientific methodology. What observations actually led to the solutions? What can mislead a researcher ?

Now back to the class, The proposed wisdom was that we should treat our fellow researchers nicely when they make wrong claims. If you have to disagree then articulate it in such a way such that you wouldn’t hurt her ego. This approach may serve reason(a) very well but reason(b) will be defeated. Reason(b) is much more important than reason(a). If mistakes are not pointed ruthlessly then correctness of science can be in danger. Researchers will not feel pressure to make correct and exact statements.

It seems asking point-blank questions is considered bad behavior. You can’t say on someone’s face, “You are wrong”. As Richard Dawkins noted as “Nineteenth century taunt” in his book “The God Delusion”:

“My whole world-view was condemned as ‘nineteenth century’. This is such a bad argument that I almost omitted it. But, regrettably I encounter it rather frequently……..
… What ,then, is coded meaning of ‘you are so nineteenth century’ in the context of religion? It is code for: ‘you are so crude and unsubtle, how could be you are so insensitive as to ask me a direct, point-blank question like “Do you believe in miracles?” or “Do you believe Jesus was born of a virgin?” Don’t you know that in the polite society we don’t ask such questions? That sort of question went out in the nineteenth century.’ But think about why it is impolite to ask such a direct, factual questions of religious people today. It is because it is embarrassing! But it is the answer that is embarrassing, if it is yes.”

The sentence I want to pick is “it is embarrassing!”. What is the equivalent in academia? In academia, If someone proves that you are wrong then it is embarrassing movement for you. It is totally opposite to what scientific methodology asks you to behave. Let me quote Dawkins again,

“I have previously told the story of a respected elder statesman of the Zoology Department at Oxford when I was an undergraduate. For years he had passionately believed, and taught, that the Golgi Apparatus (a microscopic feature of the interior of cells) was not real: an artifact, an illusion. Every Monday afternoon it was the custom for the whole department to listen to a research talk by a visiting lecturer. One Monday, the visitor was an American cell biologist who presented completely convincing evidence that the Golgi Apparatus was real. At the end of the lecture, the old man strode to the front of the hall, shook the American by the hand and said–with passion–“My dear fellow, I wish to thank you. I have been wrong these fifteen years.” We clapped our hands red. No fundamentalist would ever say that. In practice, not all scientists would. But all scientists pay lip service to it as an ideal–unlike, say, politicians who would probably condemn it as flip-flopping.”

That is the highest ideal of science. If someone claims that you are wrong then, after understanding your mistake, you should accept it and enjoy the correct knowledge you have learned.

[Somewhere i had read that one shouldn’t write post longer than 1.5 page long otherwise no one will read. So,
To be continued….]

Categories: Science Tags: ,