rise and fall of p-value: a lesson to be learnt.

Last year, after many years of p-value abuses, the american society of statistics in a revolutionary move published an instruction on how to use p-value. YOU HAVE TO read this before hand, if you ever gonna use p-value. But, here I want to pay attention to a more general mentality, which I believe is the caused of this misuse of p-value.

Since you may not have enough time to glance over the paper, let me just briefly summarize my understanding in few words, although this does not replace the whole manual. It basically says that the value of p-value for large p, does not have any significance by itself. Whenever, p is less than a particular threshold (say <0.05) then we can say that it is less likely your data with a true null hypothesis. Or more scientifically, you can strongly reject the null hypothesis, that is, there is an effect (null hypothesis is assuming that there is no effect). However, the size of effect is not determined by p-value. Additionally, you should always consider that the unusualness of your data.

In modern science, especially, during last 50 years numerical value became more important than ever. Previously, we had qualitative and quantitative understanding, now the former is losing the race to the quantitative universe. Crudely speaking, for me quality is not necessarily non-mathematical or numerical, but something that you can not specify it with a finite set of numbers. IQ, SAT score, GPA are just a few examples of many, which is a single number to specify Intelligence, or Academic preparedness, or academic valuation of someone (which of course, is a sham). In this particular universe, only (finite) number matters, and it usually take while to come up with a good MEASURE which turns multi-variate systems into a single (or a few) number. In particular, dealing with large set of events and data, is one of those areas that turning knowledge into number is usually hard. So the measure, such as p-value come to rescue!!

Now, all scientist in life sciences, environmental sciences, and psychology who does not want to spend enough time to study to understand statistics with underlying assumptions, just take the equation and leave the rest (it is always said: the devil is in the detail). Few years ago, there was a research paper titled: “Why Most Published Research Findings Are False”  which was really disappointing, later on there was very depressing while courageous statement in Nature article in 2014, by Steven Goodman (statistician@Stanford) stating that: “The wake-up call is that so many of our published findings are not true.”.  In the light of these findings, most likely we should rethink and reevaluate all those suggestions by FDA and other agencies, which are heavily based on those studies! The depth of disaster is so deep that nobody wants to even scratch the surface.

Anyway, I do suggest not only restricting the daily usage of p-value, but also leave the whole mentality that everything can be turned into a single number! Sometimes, it is just more than that. I don’t say we should not try to understand things quantitatively, in contrast, what I am saying is that sometimes quantifying with a single number is over simplification and underestimate the reality.

 

خلاصه سه ماه زندگی در ایران

با سلام خدمت دوستانم،

مدتی بود که از فضای بلاگ نویسی فاصله گرفته بودم و با اینکه دلم میخواست که گزارش کوتاهی از هر روزم ارائه کنم، تا به امروز این گزارش لحظه-به-لحظه امکان پذیر نشده. همونطور که برخی از دوستان میدونن، من مدتی است که به قصد رصد کردن اوضاع به تهران برگشتم. شاید خوب باشه که یک پست مفصلی راجع به دلایل این تصمیم بنویسم، ولی به صورت خلاصه هدف اصلی این هست که اگه فضای کسب و کار و زندگی طوری باشه که بتونم تجربیاتی که کسب کردم رو درشهر خودم به انجام برسونم، چرا نکنم؟ البته شاید من تجربه خاصی داشتم، مثلا استاد من آلمانی بود وبا اینکه موقعیت خیلی خوبی تو کانادا داشت برگشت به آلمان، و در یکی از شهر های نه چندان معروف شروع به کار کرد، البته پیشنهادات خوبی به ایشون ارائه کرده بودند. همینطور، استاد پسا دکتری من هم که یک کانادائی فرانسوی زبان بود، با اچ ایندکس ۴۴ و بالای ۱۲ هزار ارجاع، با اینکه میتونه در هر دانشگاه تراز اولی داخل آمریکا شغل بگیره، تصمیم گرفته بود که به شهر کوچیک خودش تو کانادا برگرده و تا به امروز تاثیرات بسزایی در رشد دانشگاه خودش داشته؛ برای مثال، فقط پارسال، ۳۳ میلیون دلار فاند وارد دانشگاه کرد. سوالی که از خودم پرسیدم این بود که من که با اینها قابل قیاس نیستم، اما چرا اینکار رو امتحان نکنم! البته میشه خیلی جوابها داد، ولی قصد این پست توضیح یا توجیح نیست و فقط  بازنگری ۳ ماه گذشته است.

هر چند که شاید ۳-۴ ماه مدت کافی برای جمع بندی دقیق نباشه، ولی میشه احساس نسبی رو منتقل کرد. اول باید بگم که این متن من رو با این پیش فرض بخوانید که من مشکل مسکن که از مهترین خرجهاست و شاید دقدقه خیلیهاست ندارم. این گزارش به چند بخش دانشگاه، ادارات، وجامعه تقسیم میکنم:

دانشگاه

 در بدو ورود، با توجه به هماهنگیهایی که از قبل انجام داده بودم،  در یکی از بهترین دانشگاه های ایران با سمت استادیار مهمان مشغول به کار شدم.  راستش چون از ۶-۷ ماه قبل،  تمام مراحل درخواست و پروپوزال و غیره رو طی کرده بودم، و با همکاری شبانه روزی بنیاد نخبگان، این قسمت خیلی سریع پیش رفت. حقوق ما از طریق بنیاد تامین میشه که چیزی حدود ۳.۵ میلیون در ماه است. بقیه قسمت های دانشگاه از بخش امور اداری گرفته تا هر بخش دیگه ای کارها به کندی تمام صورت گرفته و خوشبختانه هیچ تفاوتی بین ما و بقیه قائل نشده و کارهای ما هم مثل بقیه به راحتی عقب میندازند! اگه حمایتهای رییس پژوهشکده نبود تازه از این هم بیشتر طول و عرض داشت. کلا من به عنوان استاد، این بار، محیط دانشگاه رو بیشتر از پیش خمود و بی تحرک دیدم. البته چیزی که این وسط نوید بخش بود حضور دوستان دیگه و همچنین فعالیت های نسل جوانتر بود که شاید قبلا دیده نمیشد. البته این هم باید اضافه کرد که، از اونجائی که من در زمینه علوم و مهندسی کامپیوتر کار میکنم، شاید این امر طبیعی باشه، و شاید در رشته های دیگه همین تحرک هم  کمتر دیده بشه؛ باید از دوستان دیگه در این زمینه نظر خواست.

ادارت

ادارات هم مثل قدیم فرسوده و نا کار آمد هستند، یعنی هرجا که گذرت بیوفته، احساس میکنی که پشت سر کارکنان اون اداره اسلحه گذاشتند و به ضرب و زور آوردنشون سر کار. تو اتاقشون نیستند، جواب نمیدند و تکریم ارباب رجوع نمیکنند. شاید یکی از بدترین تجربه های من تا به امروز از وزارت علوم بوده. البته برای من سخته که نسبت به قبل مقایسه کنم، چون خیلی یادم نیست که قدیم چه جوری بوده(فقط یادمه که هر کاری ۲-۳ روز اضافه تر طول میکشید). به هر حال، از سیستم اداری در کل جهان نمیشه خیلی انتظار داشت، ایران که جای خود داره. بزرگترین مشکل از گذشته تا به امروز شاید این باشه که تو ادارات سر در گمی زیاده. کسی نمیدونه کجا باید بره و یا چه کاری رو باید الان انجام بده، و برای کارهاش باید چی به همراه داشته باشه. در واقع فرایند کار باید به صورت دهان-به-دهان منتقل بشه و ادامه پیدا کنه، والّا  اگر تصور بر این هست که دفترو یا وبسایتی هست که بشه استفاده کرد، نیست.

جامعه

در مورد جامعه ایران صحبت کردن خیلی سخته، حتی جامعه شناسها هم در توضیح رفتار این قوم خیلی با قطعیت نمیتونند صحبت کنند، چه برسه به من که سر رشته ای هم ندارم. ولی در حد یک ناظر چند ماهه، بزرگترین مشکل مردم ایران خودشونند. این موضوع من رو همیشه یاد دعایی میندازه که میگه، خدایا! من رو از دست خودم نجات بده. تقریبا کسی رو ندیدم که به هیچ نوع قانونی احترام بذاره و رعایت کنه، از قوانین راهنمایی رانندگی گرفته تا قوانین کار، تا دستور پزشک!  یعنی تقریبا رابطه بین قوه مقننه و مردم قطعه، انگار اونها دارند واسه یک کشور دیگه قانون گذاری میکنند. منصفانه بنگریم، قانونها خیلی هم محدود کننده تر از جاهای دیگر نیستد، ولی مردم تمایل به عمل به هیچ قانونی ندارند. اگه از من بپرسی مردم یکجور هرج و مرج طلب هستند ولی در حرف همشون عاشق نظمند! این تضاد چیزیه که مردم ما رو از بقیه جدا میکنه!

الان که از بالا به پایین پست خودم رو خوندم به نظرم اومد که هرچی بدی بود گفتم، حالا وقتشه که راجع به خوبیها هم بگم. چیزی که آدم رو امیدوار میکنه اینه که در همینجا کسانی هم  هستند که دارند خوب کار میکنند و نیات خوبی دارند. چیزی که آدم رو به جلو میبره وجود افرادی است که هنوز به پول به عنوان مقصد نهایی نگاه نمیکنند، بلکه اون رو فقط یک ابزار میدونند. هنوز کسانی هستند که به آموزه های چند هزار ساله مشرق زمین اعتقاد دارند و اونها رو در پیش می گیرند. چیزی که شاید کمتر جاهای دیگه دیده بشه. در ضمن، از لحاظ کاری،  فضایی باز شده که  شرکتهای خصوصی درحال پیشرفت هستند، البته دوباره تاکید کنم که این بیشتر در زمینه علوم کامپیوتر و پزشکی دیده میشه. به هرحال، از فضای قدیمی، جوانه های تغییر به سمت جلورو میشه دید. این تغییر فقط در فضای خصوصی نیست، و حتی تو فضای دولتی هم نگرانیها به روز شده، برای مثال، چند وقت پیش طرحی تصویب شد که تولید، واردات، و عرضه محصولات ترا-ریخته ممنوع شد! چیزی که شاید هیچ وقت در آمریکا امکان پذیر نباشه. وقتی اینها رو کنار موضوعات شخصی، مثل خانواده و چیزهای دیگه قرار می گیره، می ارزه که در همچین فضایی تحرکی انجام بشه. به هر حال، به عقیده من، هر کسی به دنبال تغییر و بهبود هست، باید سهم خودش رو بپردازه و درحال  حاضر، با حمایت بنیاد ملی نخبگان و آدمهای مثبتی که در دانشگاهها و فضای کار ایران هستند، این امکان فراهم شده، فرصتی که شاید قبلا نبود

 من اعتقاد دارم که به جای اینکه صحنه رو خالی کنیم و جامون رو به  آدمهای خشک و قانون شکن بدیم باید در صحنه بمونیم و اونها رو یا  تغییر بدیم یا از صحنه بیرون کنیم. در واقع اگر برای نسل من، همون دهه شصتیها، فرصتی باشه اون فرصت همین الانه! و یادمون باشه که بچه های نسلهای بعدی هم دارند تو همین فضا بزرگ میشند و نباید از اونها انتظار اعجاز داشت. واسه همین، هر کار مثبت یا منفی تا چند نسل پس لرزه هاش تدام خواهد داشت.من هم مثل خیلیهای دیگه اعتقاد دارم که خوبی و بدی مسری است، و اگر تعداد خوبها به یک تعداد بحرانی برسه، گذاری صورت میگیره که به نفع همه مردم ایران و جهان خواهد بود.

Why Do Many Reasonable People Doubt Science?

Some days ago, I read an article in the national geographic website, with the same title (here). This article first starts by stating that people, even scientists, ignore science since in accepting scientific facts we “cling” to our “naive beliefs”.  There are several examples, in the article which the author argues they are just scientific facts, but people have the hard time believing in them, simply because human nature is naive!

Recently, I came across several articles with the same type of logic, and discussions about the “naive beliefs”. I find the reasoning used in this article and similar ones ridiculous. In another post, I explained what is wrong with “scientific facts”. However, please let me explain in some more details why people doubt science. First of all, it happened to all of us when we started our day by looking at the weather forecast. However, once we looked outside, we saw something completely different! So you could obviously see there are many unexpected things that can happen which was not included in our scientific models. Everybody sees this shortage and understands that, particularly, when we are dealing with large multivariable systems.

Somewhere in the article says that “We’re asked to accept, for example, that it’s safe to eat GMO (genetically modified organisms)…because, the experts point out, there’s no evidence that it isn’t and no reason to believe that altering genes precisely in a lab is more dangerous than altering them wholesale through traditional breeding.” This statement is wrong at so many levels.  First of all, when we are talking about our health we tend to stay close to our tradition simply because we know that it has been working fine for many many years. Second, I have seen no clear data to rule out the correlation between these many new diseases and GMOs. For example, we don’t know at what time scale we should expect to see the correlation. It may take more than 10 or 50 years for something to affect us.  Or even worse, it is not clear for what type of disease we should look for. Finally, we don’t know what could be the effect of GMO on environment, the time scale for the environment could be much longer than 50 or 100 years. Just as an example, look at the history of DDT. 

People doubt science due to the failures of science throughout the years, not because they cling to their naive beliefs. They doubt science because of many things that can go wrong in one scientific research. As I emphasized in previous posts (e.g., here),  science is not for believing, but it is a process to falsify our understandings. I should say, although I agree that scientific process is the only trustworthy method to investigate each and every question, we have all the reasons to doubt “scientific facts”, particularly those sciences which rely heavily on statistical inferences.

Why there are many stories, metaphors, and proverbs in religious texts?

It doesn’t matter which religion, in all of them you see storytelling, and extensive usage of metaphors and expressions in communicating a message.  When I was learning writing in English, I was told that I should write concise short sentence with a clear message, and try to avoid any complication in delivering my message. Compared to what I learned, the religious texts are way off!  The question is why? Why in communicating spiritual messages we urge to use stories, instead of directly cutting into the chase. As a Persian, I can name several well known books by religious authors which are filled with delicate religious stories. Ancient Persian poetry is also famous for that. There are thousands of pages written with high caliber of ingenuity just to deliver simple spiritual messages!

I have been puzzled by this question for a while. Now, I believe that I understood why that’s the case, and I try to express my understanding with minimum complications. To answer this question, let me start by answering a similar mathematical question. How can one explain a three-dimensional object with the two-dimensional mathematics? The best way is to slice it up to many two-dimensional surfaces and then introduce each and every surface, one by one. For example, introducing a simple tree to a 2D universe, needs many (infinite to be exact) layers of 2D images. So, as you see whenever we aim to explain even a simple object, but from a higher dimension, we would face a challenge.

In another example, how one can explain the taste of an apple (say McIntosh) to a society who have never had an apple in their life! The first step is to find out what type of taste that particular people are being exposed to. Then the idea is to mix different tastes to get closer and closer to the taste of apple. So, this is exactly the process of delivering something which does not belong to our ordinary common senses.

In the spiritual world, I believe that is the same. Once a person observe something which does not well fit in our current realm of understanding, one needs to slice it up to many different little stories where the role of each of this stories is to lighten up one side of the observation. For the sake of this conversation, I don’t mind if the origin of this observation is due to the ecstasy of meditation, or due to some chemical compound.  What I do care, in this post, is that sometimes a simple observation requires a lot of explanations, simply because it doesn’t belong to our everyday life experiences, and yet you can not make the point exactly.

How natural is our mathematical world?

Looking at the geometry, we instantly realize that we are used to assume everything is composed of straight lines. Or the mathematical analysis is full of linear assumptions here and there. However, in reality finding a straight line or a linearly interacting system is almost out of reach. This difference may seem  abstract at the first sight. However, the effect of our mathematical assumption is perfectly vivid in manmade products, such that, by looking at a particular object we could easily distinguish manmade from natural. This deviation is clear since all of manmade products are engineered based on the mathematics that does not share the same symmetry with the nature around us.

This is also true, for our modeling. All of our models are linear interaction model, which absolutely is far from what happen in the real life. As it is nicely mentioned by Wigner, we are so lucky that our models can roughly explain what happen in the real life. Additionally, This type of thinking is not limited to the science or the engineering, but it is also extended to the social sciences such as philosophy. We should understand that sometimes what we call perfect or ideal, is not necessarly the ideal of nature around us. We should also note that what we learn in the school is not necessarily what happen in the world.

I finish this post by asking, can there be a different mathematics, more inline with the nature, where we can relax a straight line or linearity assumptions?

 

رعایت قانون اختیاری نیست

اخیرا موضوعی رو خوندم که توش اشاره داشت که اما بنینو، وزیر امور خارجه ایتالیا در هنگام ورود به ایران اصرار داشت که بی‌ حجاب وارد شه. صرف نظر از اینکه آیا شخص بنده با روسری اجباری موافق یا مخالفم، به نظرم کار ایشون یخورده غیر منطقی‌ و خارج از شئونات دیپلماتیک بوده، و در واقع احساسی‌ عمل کرده. از آونجایی که برخی‌ هموطن‌های ما هم دچار این مباحث میشن، دوست دارم که نظرم رو راجع به این موضوع بیان کنم.

خانوم اما بنینو باید این مساله رو درک کنه که حجاب در ایران از بحث فقهی‌ و مذهبی‌ خارج شده و به بحث قانونی تبدیل شده، و رعایت قانون بر همگان بویجه افرادی که وارد ایران یا هر کشور دیگه‌ای میشن لازم الاجراست. مثل اینکه، بر فرض داشتن سلاح تو کانادا غیر مجازه، و یه آمریکایی بگه من می‌خوام با کلتم وارد بشم.

در ادامه ظاهراً اشاره شده بود که وقتی‌ که دیپلماتهای ایرانی‌ به کشورهای دیگه میرند، کشور میزبان به احترام اونها مشروب روی میزا نمی‌گذارند. این نشان فرهیختگی اون کشوراست، ولی‌ باید باز اشاره کنم که گذاشتن شراب روی میز یه بحث عرفی در خارج از ایران هست، نه یه بحث قانونی، در حالیکه پوشیدن حجاب یک بحث قانونی در ایران هست.

اینکه حالا چرا حجاب اجباریه، و چجوری می‌شه عوضش کرد و غیره کاملا بحث‌های جدایی هستند که در جای خود باید نقد بشند. ولی‌ این نکته مهمه که درک کنیم، در هر کشوری زندگی‌ می‌کنیم، یک سری قوانین هست که ما با اونا مشکل داریم، ولی‌ مخالفت ما به ما حق عدم رعایت قانون رو نمیده. بلکه ما باید در چهارچوبهای قانونی تلاش کنیم که اون قانون به سمت بهتر شدن حرکت کنه.

“click”

There have been critical moments in our life when we wanted just to get over it, either it is an exam, or defence, or a promotion, citizenship, etc. On the other hand, this is our life which is passing by, so we want it to slowly moving forward. There is an interesting movie illustrating these two competing features of our daily life: http://www.imdb.com/title/tt0389860/?ref_=tt_rec_tt . The style of movie is a little bit childish, however, the bottom line message is for all adults. I encourage everyone to watch this movie. Here is my my favourite quotes from the movie:

1) it seems that whatever I do, I disappoint someone. You have to make sure that you are not disappointing the wrong people.

2) they are Japanese, they can’t wait for a fish to cook.

Gender equality in Persian language.

I believe that language is the first intellectual creation of human being. Looking at different languages, there are several similarities and differences. One of those similarities between many languages such as English, French, and Arabic is that they are gender biased. It means that making a non gender biased statement is almost impossible. There are always some prefix or suffix to determine the nature of the “subject” or “object” as masculine or feminine.

In persian language you do not have this issue. There is almost no determinator of gender in the verbs, names or adjectives. So, each sentence is equally applicable to both males and females unless it is specified. I believe that this fact refers to the gender unbiasedness of ancient Persians. I do not have much studies in this field, however, I am planning to read more in this direction to understand better the issue of gender (in)equality in different languages. So, stay tune.

Every person is innocent but a suspect!

The most common legal right of a human being is the presumption of innocence, which means, one is considered to be innocent until proven guilty. I think, the interpretation of this principle is very tricky nowadays. There are several approaches and attitudes toward this principle for national and international securities. Previously, innocence of citizens was assumed, so no one had the right to collect personal and interpersonal information without the person’s permission.

However, the new approach, apparently, is that, everybody is innocent but a suspect! Hence, all the information should be gathered in order to prove the sin when it is necessary. Facebook, google, yahoo, and almost all other online and offline companies are basically carriers to transfer our information for marketing and, of course, other purposes. Thanks to Snowden we are well aware of other purposes of this stored information. Very soon there will be a time when everybody is living in a society with transparent walls (of course, transparent only to some people) and is analyzed by people who can see through them. Not long from now, the information of our living habits would be a tool in governments hands not only to control us but also to shape our behaviour, in the direction of their interests.
We are already living in the era of pre-determined paradigms such that we believe those paradigms are discovered by us, and we have no doubt about them. For example, the idea of success, patriotism, human rights, work, education, etc. In future, or maybe already, paradigms will be also shifted by the governors, while it is believed by the people of the society that they are responsible for making the shift (like “The Truman Show”). It is a simple strategy: people act based on their beliefs. By controlling and manipulating the belief system, one can control everything while giving a false impression that there is no control. I would call this new era: the era of ” adiabatic paradigm shift”.

Possibilian: from fundamentalism to atheism

Thanks to Ali jan for sharing this nice ted talk with me. It is an inspiring talk and this is one of those subjects that I wrote something about, e.g. here or here. To start, in my opinion, he touched two interesting points, first, he clarified that our belief system is a byproduct of our cultural system, and second, he gave a good description of “what really the science is”.
His main message was: listen to all ideas, filter them by the toolbox of science, and then consider the other possibilities. Finally, he emphasized on staying away from making a strict choice when there is a little known and a lot unknown. That’s very good and nice, however, there are several drawbacks here:
1) We live for a rather short time and during this time we are forced to make a decision about some main fundamental questions  (no matter how much we understand), from which almost all religions are coming from, such as where are we coming from, where are we going, and why are we here! How we answer them would change our behaviour in this very world during our short life span. Willingly or unwillingly we are answering to those questions and behaving accordingly.
2) He also nicely mentioned about the role of science as a filter, however, he did not emphasize that science by itself is an ever-changing land of possibilities which open-minded-ly contradict itself from time to time. It means that the toolbox/filter by which we falsify other theories sometimes is changing so drastically that some of the impossibles become possibles and vice versa. For example, in life science, before the discovery of DNA, it was so absurd (scientifically) to talk about a fundamental quality which is transferred from parents to children (called fetrat in Islam) which would determine the most of child character! However, nowadays, it is believed that almost everything is inherited from parents, and education, societies, etc can do a little to change that! So, basically, science is making random walks in the phase-space of possibilities.
3) The way the decisions are made in his “possibilian” approach is biased towards science, so I would rather call this new religion as scientism. Since, the righteousness of possibilities are measured with (modern) science and not the other means. Of course, there exist other possible toolbox/filters. For example, to treat a certain disease you may choose to use modern science or ancient medicine. So, possibilian is rather a larger pool than what is explained in the talk!