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It’s been a while since my last post but I have lots of excuses. I have found a job and now I am working as a software engineer in Företagsplatsen, a small company with huge expertise and ambition. Our lovely office is located at Gamla Stan(I couldn’t imagine working at an office there before). We have a great team of developers and sales people.

I got my work permit after a long and troublesome process. The process was preventing me from visiting my girlfriend for many months. Truth to be told, I still feel angry when I think about the case officer and her behavior for my application. But with great relief, it is over.

I had the chance to visit my girlfriend during Christmas after I got my work permit. Seeing her after a long time was the happiest moment for me for 2015. When I arrived at the terminal station in Kadikoy, my heart was literally pounding. I was so happy with her during those days; when I look back, I feel nothing but regret leaving her in Istanbul(Unfortunately, it was the logical thing to do). But I had another chance to visit her during February for a week and we will be visiting Lisbon(my girlfriend’s favorite city and my previous home) in June. Even if we have some troubles in our relationship right now, she is the one that makes me feel incredibly happy.

Unfortunately, I have little time for my thesis work so it is now on hold for some time.

I plan to write more from now on.

As a part of my thesis, I’m assigned to integrate Java Batch Processing(JSR-352) into Hops. The problem I need to solve is actually simple : How can you create a JSR-352 job dynamically and then submit it?

Everything started in a cold Stockholm day, I was reading JSR-352 specification and giving my best to understand it. With every page and every sip of tea, my curiosity was growing bigger and bigger. Something was not right! I turned the last page, read it quickly and it was done. YAY, THE ONLY WAY I CAN SUBMIT A JOB IS TO READ FROM A FILE! YOU KIDDIN ME!

Well, I found a workaround. It requires a string containing the xml file’s contents. In other words, you can submit jobs if you have a string describing the job itself in proper xml. I give you the class definition with a static method which runs the job based on the input string. Beware that you should add proper dependencies (for example, using Maven) for Jbatch into your project in order to make it work.

import com.ibm.jbatch.container.services.IBatchKernelService;
import com.ibm.jbatch.container.services.IJobExecution;
import com.ibm.jbatch.container.servicesmanager.ServicesManager;
import com.ibm.jbatch.container.servicesmanager.ServicesManagerImpl;
import java.util.Properties;

public class JobStringRunner {
    
    public static long runJob(String xml) {

        Properties props = new Properties();

        ServicesManager servicesManager = ServicesManagerImpl.getInstance();
        IBatchKernelService batchKernelService = servicesManager.getBatchKernelService();
        IJobExecution jobExecution = batchKernelService.startJob(xml, props);
        return jobExecution.getExecutionId();
    }
}

This is a lengthy guide to use adam-shell in Apache Zeppelin.

Adam is a library for exploring and manipulating genomic data. It is quite popular among people who spend their life trying to create horse-sized ducks and then duck-sized horses. To help them achieve their goals, here is a short guide for using Adam library in Apache Zeppelin.

One of the main reasons of Adam’s popularity comes from the fact that it is actually developed as a custom API on top of Apache Spark. So with some distributed computing knowledge, it enables you to use your computing cluster to full extent.

What is Apache Zeppelin? I really don’t want to define Zeppelin because it is hard to define as a whole. In very simplistic terms, it is a web based notebooks for whatever interpreter you have. Luckily we have Spark interpreter since the beginning of the Zeppelin as an incubating project under Apache umbrella. So how can we use Adam library in Zeppelin?

If you know Spark to some extent, you try to put jar files of Adam libraries into appropriate locations then configure you Spark setup to load them on start-up. Then you start to hope that when Zeppelin starts and creates Spark environment for you, everything’s gonna be OK. However, you are not a computer scientist. You don’t care about Spark configuration gimmicks. What should you do?

The answer is actually simple. Zeppelin also comes with a dependency loader.

%dep 
z.load("org.bdgenomics.adam:adam-core_2.10:0.17.0")

If you get an error message saying that dependencies should be loaded before running spark interpreter, then you need to go and restart spark interpeter and try again. If you get a valid result, then you are good to go. What the lines above does is to fetch Adam library from maven repositories and load it into your environment. I don’t think I need to explain how can you get the different versions of Adam library with the same method.

Whatever you do with adam-shell, you can now do it with Zeppelin and enjoy Adam-Zeppelin integration while creating duck-sized horses.

Go my friends, create the next horse-sized duck and name after me!

HR People of the planet Earth, please unify the job application systems! Come on!

Last few days, I’ve learnt to submit my profile in hundred different ways.

I need a job to ensure population balance,specifically for my survival.

For my philosophy of science course at KTH, I had to submit an essay. I started writing few days before the submission, but I managed to submit it on time. Moreover, I got an A! This is the first A(I hope not the last one) for me at KTH.

I should thank my girlfriend, Melike. Without her editorial help and suggestions, this essay would be no more than some random words with semi-proper grammar.

Need for a New Scientific Transformation, Applicable to Science Itself

An essay about line of demarcation, creation-science and methodology of science

Science and religion often seems to challenge each other. Possibly the most common example explaining the situation is given such: Gods surely punish us by sending lightning, flood and diseases. However men of the 21st century often thinks electrical discharge, climate change, and lack of health-care is also probable. Debates when science and religion share the same table is not uncommon. There were and are people on both sides claiming victory for the name of either side. However, without an authority, most of this victory chants cannot be just. Yet, one of the clean victories of science against religion could be considered the fundamental place of evolutionary ideas in modern biology. Although National Center for Science Education indicates that they don’t wish “to mislead the public into thinking that scientific issues are decided by who has the longer list of scientists”, their steve-o-meter reads 1352. Implication of the project Steve is that overwhelming majority of the scientists are in favor of evolution, hence of science. We understand the concerns aimed with the warning above. This warning itself will be revisited when I mention about Lakatos’ ideas about science. However, that warning is not my main topic in this essay.

Evolutionary ideas are challenged by so called creation-science or intelligent design. Supporters of creation-science often present evolution and creation being alternatives thus teachable in public schools side by side. For example, a book from creation-scientists, Of Pandas and People is suggested to be a reference book in some public schools (US legal case: Kitzmiller v. Dover Area School District ). Even if legal cases such as the former one and notable McLean vs Arkansas case resulted in favor of science, the situation has to be investigated in philosophy of science. Moreover, those legal cases faced several criticism. There is no ultimate satisfactory decision for both parties on the matter and it is very unlikely to ever be.

The crucial question that is to be asked concerning the issue on the never-ending conflict between religion and science is as the following: How do we decide what is scientific or not? Usually bin analogy, a method which is used in categorizing things, is used. So we can decide the faith of creation-science by creating a hypothetical bin for science. We pick a bin to put everything scientific in it, and immediately our selection process becomes a round table discussion featuring Karl Popper, Thomas Kuhn, Imre Lakatos and many others. The problem arises when we try to decide if something is scientific. It is not easy to categorize into something as science. There is no consensus between philosophers for a science definition or line of demarcation.

According to Popper (Curd & Cover, 1998, p.3-10), scientific theories should be falsifiable. There should be some probable setups that the theory would be proven wrong. Popper suggest that risky predictions have to be made by scientists. There is no science if your theory doesn’t take any risks. And scientist should make experiments to falsify their theory with the risky nature that the theory which it should contain. Eddington experiments are given as a common example. If the shift of sunlight had not been compatible with the Einstein’s predictions, theory would had been falsified. It should also be noted that Popper considered the principle of natural selection in theory of evolution pseudo-scientific for decades until 1977 (as explained by Curd & Cover, 1998, p.65).

On the other hand, Kuhn (Curd & Cover, 1998, p.11-19) objects the utopian picture that Popper depiction of daily work of a scientist. Scientist doesn’t try to falsify theories every day. He came up with “Normal Science” to define the periods where scientist doesn’t try to falsify theories but use them to solve puzzles. Puzzle-solving is the main act in science. According to Kuhn, there are special periods when “normal science” becomes “extraordinary science” where scientist start to challenge and falsify current theories like Popper suggests. Kuhn suggests that these revolutions happen when puzzle-solving sessions result in failure repeatedly by a considerable amount of scientist. This situation leads to a crisis and welcomes the period of extraordinary science. Kuhn states that extraordinary periods are rare, short but revolutionary periods. Kuhn’s approach heavily depends on the people who are doing science. Going back to the warning in the first paragraph, if all scientists are in favor of a theory then it should become scientific. If we look at the opposite case, it also means that scientific theories are not scientific if there are no people in favor. This approach couples scientific value of theories with scientists in that field.

Thirdly, Lakatos (Curd & Cover, 1998, p.20-26) doesn’t think that science has revolutions as Kuhn suggests. It’s a slow process so not a revolution. In addition to this, Lakatos also notes that knowledge cannot be considered genuine in terms of their number of supporters or their strength. He considers science as several “research programmes”. Those research programmes contains core theories, together with hypotheses that acts as protective belt, and finally a heuristic to approach to the problems. Lakatos’ depiction of research programme fits with the common practice of the scientists. They don’t easily abandon the theory, they just mark the current result as anomaly. So research programmes are lengthy process for doing science. Between competing research programmes, degenerating ones lose their scientific status and improving ones become a part of the science.

With creation science and a short introduction to discussions about line of demarcation, one can start the process of deciding whether creation-science is a genuine science. Yet as it can be deduced from multiple views mentioned above, it is not a trivial job. In addition to this, no negative answer seems to satisfy religious sides. Religious bodies have a long run of touching scientific areas and supporting their holy theories. At the end of the day, we are pretty sure to find someone claiming that creation-science is a genuine science and there was a global-scale deluge that we should mention in biology class when we talk about species. Are those people stubborn? Or fanatic? Do they subject to some holy revelation that we poor souls have not experienced? What makes them resubmit their ideas to discussion for their scientific status, even if they mostly come from religious scripts, which usually advertised as unchanged/well-kept? We cannot go any further if we assume they are just stubborn or fanatic. Truth to be told, a revelation might be a good idea. On the contrary, defining the creationist is not a good idea. It seems like we started to define everything related to science in order to define science. Honestly, it looks like an overkill. Then what is the next step in our discussion? Rather than defining science, or scientist, or creation, or creationist; what can we do in order to achieve our goal? In my approach, rather than working with definitions, I investigate a possible line of demarcation that science can fit in and then approach science to transform it to in the space that line of demarcation restricts. That criteria should silence creationist claims without marginalizing or shrinking science.

If we will transform science into something, why not transform it in a way that it will have no similarities with religion? It seems to be a very good idea. Without similarities, they will sure to be separated. But in the current context, what are the similarities that enables creationists to advertise their claims as scientific? There are several similarities in methods.

The striking similarity is how we present science in public schools and how religious claims are presented in general. It is also a perfect start point since we want to prevent creationist claims entering public school biology curricula. Religion in general and public school science is often presented similarly. Biology teacher presents evolution in the classroom in a similar way that a priest teaches the genesis. An unquestionable authority presents the information in both cases. Teacher or priest says the last word, not students. Often examples are simplified in classroom to facilitate learning process. And the priest tells a similar one: The god also simplify things in order to be understood by us. The material in use is not open to question, either. You just get your textbook that the teacher asks, you don’t make a choice. You don’t decide between Bible and Quran, you just “pick” the “right” one. Students don’t have any power on selecting materials at all. How to find necessary material is not even shared with students. They, modern biologist and creationist, seem to teach different scientific alternatives to students because they follow very similar ways. An idea behind a story about Galapagos Islands (where Darwin studied endemic species) is comparable to an idea behind Lot and his sisters, isn’t it? They want to make a point and they use stories in order to achieve it.

Students intrinsically assume that teacher knows more than them. Public school student or religious one shouldn’t question the overall topic, but they are allowed to have questions and misunderstanding. Things that are not explained in classroom is assumed to be hard to be understood by students. They are assumed to be just ignorant students with little information. The consensus is that they cannot know what they cannot understand. God also does the same. The priest also tell us if that divinity doesn’t mention something, either it is none of our business or we are not able to understand it, and sometimes both. In my opinion, this similarity of underestimation is one of the key reasons that creation can pretend to be a genuine science if allowed. Moreover, this also confuses the legal authorities for decision making when creationists’ claims are present. And the last but not least, the ideas they present is advertised to be utmost important. The students will have an exam and one of the questions will be about the story. That is also taught that we will also have an exam for the afterlife or for our reincarnation. It is warned that we cannot simply learn and forget. We are not allowed learn it again when we want to. Preparing for the next test is their common motivation.

My first intuition was that similarity in method could be a possible source for a line of demarcation. When we look at the religion, its practicing method comes from a small set of sources and those small set of sources are usually over-sophisticated for some “unknown” reason. There is an explicit need for an instructor in religion. You might create your own religion, or you might start following one by yourself. But it is assumed that you cannot understand an existing one all by yourself. Back to my point, our hope could be to transform science in terms of methodology to create a gap, a line of demarcation. It is my proposal that we should transform scientific education for public schools. We can achieve this goal by making several changes.

The changes we can make should focus on the classroom. The very first step that we can take, the concept of teacher as an authority should be removed from science classrooms. The teacher in that setup represents a superiority. This situation is backed by the perception that teacher is perceived to know more in any topics, but this perception is trivially wrong. Moreover, conventional techniques of lecture giving strengthen this perception. In that case, a flat hierarchy could be established where teacher and students become fellow scientist working together. This could be achieved by assuming everyone as scientist by default. It is highly likely that each of them has weird individual methodologies, but it is not anyone’s job to correct it. They should discover the way to adapt, not to correct themselves.

Secondly, there should be no notion of tests or exams in science classroom. The source of test marks an authority. An authority that we formerly try to remove by eliminating the teacher’s conventional position. Moreover, test scores doesn’t promote students in terms of science. Failing or succeeding in a test doesn’t make them a worse or a better scientist, while failing a test in religion makes followers a good or bad believer. Same is also true for the positive case.

The reason behind my transformation is that the reorganization I propose seems impossible to apply in practice of religious based/inspired topics such as creation-science. First, they have a superiority by default. Secondly, a religion without lecture giving cannot disseminate its course. It can try however it would probably miss the aimed target. Other collaborative ways to learn is not applicable to religion, because it welcomes personal opinions and drifts from the source.

Creation-science claims a position side by side with modern biology, thus creationists demand an equal treatment for creationists ideas and theory of evolution. Conventional approach is to show them creation-science is not science at all by defining what is scientific and demonstrating that creation-science doesn’t qualify for that definition. However, this conventional approach is without success. There are different ideas from many philosophers on the matter of being scientific or not. Even if in the case of a possible future consensus, it is highly unlikely to prevent creation-scientists or their future equivalents to claim religious opinions as genuine science. Overall, this led me to think about a transformation for science education in public schools, where science is usually presented similarly to religion. By removing the authority and creating a flat hierarchy, science classrooms start to become places where religious ideas become alienated because of their authority and non-flat hierarchical organization. A line of demarcation is then established in this matter. That demarcation criteria says that something is unscientific if it contains predefined authorities.

This transformation of science education in public schools could separate science from creation-science. In other words differentiating science education from religious education makes the distinction between these two concepts more clear. Creation-science, which is in the latter category, then could be removed from science classrooms in public schools once and for all.

References