## A Series of Lectures on Fine-Tuning in Biology

A recent lecture and a series of interviews has been posted online where cosmologist George F.R. Ellis discusses the issue of fine-tuning in biology at considerable length and in considerable detail. Of course, the larger theme here is that to discuss and understand things like Darwinian evolution properly, one needs to have an understanding of the underlying physics, as it is laws of physics that allow life to emerge and for Darwinian evolution to occur in the first place. Here are the lectures:

## Misinformation on Sikhism

Even though this posting is a bit different than my usual ones and is outside the scope of this blog, I thought that as a Sikh myself, I have stayed too silent on several issues with regards to the Sikh community, and certain principles of the Sikh religion, that are seemingly unknown to those both inside and outside of the Sikh community. I will address here some common misconceptions and misinformation about Sikhs that are both being spread inside and outside of the Sikh community.

1. Sikhism is NOT a hybrid of Islam and Hinduism: Sikhism is a unique religion with a unique origin beginning with the teachings of the first Sikh Guru, Guru Nanak Dev Ji. Guru Nanak formed the religion to be uniquely different from Hinduism and Islam, as he opposed many of the practises common in those religions.
2. Sikhs are not to cut their hair or trim their beards. This is perhaps the most common fact that is blatantly missed by those members of the Sikh community that wish to cut their hair and propagate this misinformation to defend their actions as being accepted in Sikhism. This is a very wrong ideology for several reasons:      Guru Gobind Singh Jee, the 10th Guru of the Sikhs explicitly described the form of a Sikh in Persian:

Ik Onkaar Sri Waheguru Jee Kee Fateh || Sri Mukhvaak PaatShaahee Dasvee||

Nishaanay Sikhi Ee Haroof Panj Kaaf|| Hargiz Na Baashad Ee Panj Muaf ||

Karra Kaardo Kachh Kanghaa Bida || Bila Kesh Haych Asat Jumleh Nishaa ||

Haraf Haae Kaat Asat Ee Panjkaaf || Bi Daanand Baavar Na Goyam Khilaaf ||

HukaaJaamat Halaalo Haraam || Baachishay Hinaa Kardaroo Sayaam Faam||

Note that the usual argument that this is for the Khalsa, and not Sikhs, is patently false, as Guru Sahib explicitly says “Nishaanay Sikhi”, and not “Nishaanay Khalsa”. This point is therefore a moot point.

Guru Gobind Singh Sahib also in his Hukam to the Afghanistan Sikh sangat said:

Tusi Khande da Amrit Panja to lena

Kes rakhne…ih asadee mohur hai;

Kachh, Kirpan da visah nahee karna

Sarb Loh da kara hath rakhna

Dono vakat kesa dee palna karna

Sarbat sangat abhakhia da kutha

Khave naheen, Tamakoo na vartana

Bhadni tatha kanya-maran-vale so mel na rakhe

Meene, Massandei, Ramraiye ki sangat na baiso

Gurbani parhni…Waheguru, Waheguru japna

Guru kee rahat rakhnee

Sarbat sangat oopar meri khushi hai.
Patshahi Dasvi

Jeth 26, Samat 1756

These are not my opinions. This is explicitly the command of Guru Gobind Singh Jee. Further, the aforementioned passages also explicitly state that Sikhs are not to drink alcohol or smoke. It is truly puzzling and embarrassing why drinking alcohol has become somewhat synonymous with Sikhs, particularly, in the Punjab region.

Further, Bhai Desa Singh Jee explicitly writes the following on trimming beards:

dhaarrhaa mushh sir kaes banaaee || hai eih dhrirrh jih prabhoo razaaee || maett razaaee j sees mu(n)ddaavai || kahu thae jag kaisae har paavai

It could not be more clear, that Sikhs are to emphatically not cut their hair or trim their beards.

3. Sikhs do not celebrate Diwali. There are many Sikhs around the world that insist on celebrating Diwali, the Hindu festival of lamps. Some have even justified this action by conflating the Bandhi Chorr divas related to Sri Guru Hargobind Sahib with the Diwali day. This is also wrong for the following reasons:

For years now, I have heard this constant story of how it is acceptable for Sikhs to celebrate Diwali as per the Hindu traditions of lighting lamps, etc… Further, Raagis and Bhai Sahibs in Gurdwaras have conflated Bandhi Chorr Diwas with lighting lamps as per Hindu Diwali traditions. They further support these ideas with the supposed Vaar from Bhai Gurdas Jee, in which they ironically only mention and repeat the first line! : “deewaalee dee raath dheevae baaleean”. Of course, just by reading this line, it would suggest that the aforementioned actions are justified. But taking one line completely out of context leads one to these conclusions. A full reading of Bhai Gurdas Jee’s Vaar on the Diwali matter which given the timeframe is also a historical first-hand account suggests that Sikhs are to practice completely the opposite and in fact, lighting lamps is contrary to Gurmat. The full Vaar’s transliteration is below:
Vaars Bhai Gurdaas 19-6

diwali dee raath dheevae baaleeani

thaarae jaath sanaath a(n)bar bhaaleean

fulaa(n) dhee baagaath chun chun chaaleean

theerathh jaathee jaath nain nihaaleean

har cha(n)dhuree jhaath vasaae ouchaaleean

guramukh sukhafal dhaath shabadh samhaaleean

The essence of this Vaar is in every line after the first. Namely, in the third, fourth, and fifth lines, Bhai Gurdas Jee compares those that celebrate Diwali by lighting lamps akin to those who go on long pilgrimages to find God, and to those who search for God by worshipping the stars, or things in nature, etc… All contrary to Gurmat by a simple reading of Japjee Sahib! Indeed, Bhai Sahib Jee in the last line clearly states that a person of Gurmat does not practice any of these things, which he declares to be temporary and pointless.

So, there you have it. A simple reading of the full Vaar changes the entire context of the “importance” of Diwali in Sikhism. I doubt many Sikhs will read this posting with sincerity, but someone has to speak the truth.

4. Sikhs Do Not Eat Meat: Sikhs most certainly do not eat meat. Despite this, many Sikhs continue to insist that eating meat is permissible as long as it is not Halal, etc. This is also wrong for the following reasons:

The Sikh Gurus including the Guru Granth Sahib Jee (the present living Guru of the Sikhs) very explicitly discuss how eating meat is not for Sikhs, some examples below:

1. Guru Granth Sahib – Page 1374 – “Kabeer Khoob Khaanaa Keecharee Jaa Mai Amrit Lon, Heraa Roti Kaaranay Galaa Kataavai Kaun”.

2. Guru Granth Sahib – Page 140 – “Jay Rat Lagay Kaparay Jaamaa Hoay Paleet, Jo Ray Peeveh Maansaa Tin Kio Nirmal Cheet”.

3. The essence of why a Sikh cannot be satisfied with “Jhatka” and simply opposed to Halal is due to Guru Naanak Dev Ji, Page 468 on SGGSJ: “Daaiaa Jaanay Jee Kee Kichh Pun Daan Karay”

Several other key points are as follows:

4. “Jee Badhoh So Dharam Kar Thaapoh, Adharam Kaho Kat Bhai.

Anpas Ko Munwar Kar Thaapoh, Kaa Ko Kaho Kasaaee. (SGGS 1103)

5. “Bed Kateb Kaho Mat Jhoothhay, Jhoothhaa Jo Na Bichaarey.

Jo Sabh Meh Ek Khudai Kahat Ho,To Kio Murghi Maarey” (SGGS 1350)

6. “Rojaa Dharey, Manaavey Mlah, Svaadat Jee Sanghaarey.

Aapaa Deldi Avar Nahin Dekhey,Kaahey Kow Jhakh Maarey” (SGGS 1375)

7. “Kabir Jee Jo Maareh Jor Kar,Kaahtey Heh Ju Halaal.

Daftar Daee Jab Kaadh Hai, Hoegaa Kaun Havaal” (SGGS 1375)

8. “Kabir Bhaang, Machli, Surapaan Jo Jo Praanee Khahey.

Tirath, Barat, Nem Kiaye Te Sabhay Rasaatal Jahey” (SGGS 1376)

9. “Kabir Khoob Khaana Khichri, Ja Meh Amrit Lon

Heraa Rotee Kaarney Galaa Kataavey Kon” (SGGS 1374)

These are examples/Hukams explicitly from Sri Guru Granth Sahib Jee going back to the days of Bhagat Kabeer Jee, to Guru Naanak Sahib, all the way to Guru Gobind Singh Sahib. This is factual evidence that your claims are incorrect, and any such claims made by Sikhs that only “Halal” is forbidden, is simply wrong, as these Sikhs do not have an answer/simply ignored such aforementioned verses from Guru Granth Sahib Jee, because of a desire to not leave meat.

5. Women in Sikhism

In Sikhism, women are completely equal to men, there is zero tolerance for those men that would treat women poorly or lower than them. Indeed, according to Sri Guru Granth Sahib Jee, women are to be treated higher than men:

From woman, (man) is born; within woman, (man) is conceived; to woman he is engaged and married. With woman

(man) establishes friendship; through woman, the future generations come. When woman dies, (man) seeks another

woman; because of woman, (man) becomes related (to other people – ਲੈਣ-ਦੇਣ ਦੇ ਸਾਰੇ ਸੰਸਾਰਕ ਬੰਧਾਨੁ, etc.). From her,

(even) kings are born; so why call her bad? From woman, woman is born; without woman, there would be no one at all.  (sggs 473).

6. Sikhs and Rakhdi/Raksha Bandhan Ceremony

There are many Sikhs around the world that insist on Rakhdi/Raksha Bandhan ceremony. Sikhs absolutely are not supposed to participate in this festival. On Raksha Bandhan, sisters tie a rakhi (sacred thread) on her brother’s wrist. This symbolizes the sister’s love and prayers for her brother’s well-being, and the brother’s lifelong vow to protect her.

This very concept implies that women are weaker than men and therefore need their protection. This is in direct conflict with Guru Nanak Dev Ji’s philosophy regarding women as described above, and very much against the Khalsa Rehat, where women and men take amrit equally! Therefore, the idea that women should tie a thread to their brother’s wrist for “protection” is very much against the concept of equality, and ignores the roles played by Sikh women in history that didn’t need any man for protection. Some examples are:

• Mata Gujri Jee
• Mata Ganga Dev Jee
• Mai Bhago
• Rani Sada Kaur
• Mata Jito Jee
• Bibi Rajni
• Mata Kishan Kaur

And many, many others!

Conclusions:

The purpose of this piece was simply to stop the misconceptions related to the aforementioned points from spreading.

Further, the majority of us live in free societies, where freedom of religion is the expectation and the norm. I am a big believer in this concept, and fully appreciate having such a law in existence. This of course means that people are free to practice their religion as they see fit. However, while this principle must absolutely be firm, I question what it means for someone to call themself a Sikh on one hand and disagree with the tenets that the Sikh gurus established. This is more ironic because Sikh means “disciple”. So, you can call yourself a Sikh, but if you don’t follow the principles of the Sikh religion, what “religion” are you following?

## Mathematical Origins of Life

The purpose of this post is to demonstrate some very beautiful (I think!) mathematics that arises form Darwinian evolutionary theory. It is a real shame that most courses and discussions dealing with evolution never introduce any type of mathematical formalism which is very strange, since at the most fundamental levels, evolution must also be governed by quantum mechanics and electromagnetism, from which chemistry and biochemistry arise via top-down and bottom-up causation. See this article by George Ellis for more on the role of top-down causation in the universe and the hierarchy of physical matter. Indeed, my personal belief is that if some biologists and evolutionary biologists like Dawkins, Coyne, and others took the time to explain evolution with some modicum of mathematical formalism to properly describe the underlying mechanics instead of using it as an opportunity to attack religious people, the world would be a much better place, and the dialogue between science and religion would be much more smooth and intelligible.

In this post today, I will describe some formalism behind the phenomena of prebiotic evolution. It turns out that there has been a very good book by Claudius Gros and understanding evolution as a complex dynamical system (dynamical systems theory is my main area of research), and the interested reader should check out his book for more details on what follows below.

We can for simplicity consider a quasispecies as a system of macromolecules that have the ability to carry information, and consider the dynamics of the concentrations of the constituent molecules as the following dynamical system:

$\boxed{\dot{x}_{i} = W_{ii}x_{i} + \sum_{j \neq i}W_{ij}x_{j} - x_{i} \phi(t)}$,

where $x_{i}$ are the concentrations of $N$ molecules, $W_{ii}$ is the autocatalytic self-replication rate, and $W_{ij}$ are mutation rates.

From this, we can consider the following catalytic reaction equations:

$\boxed{\dot{x}_i = x_{i} \left(\lambda_{i} + k_i^j x_j - \phi \right)}$,

$\boxed{\phi = x^{k}\left(\lambda_{k} + \kappa_k^j x_j\right) }$,

$x_i$ are the concentrations, $\lambda_i$ are the autocatalytic growth rates, and $\kappa_{ij}$ are the transmolecular catalytic rates. We choose $\phi$ such that

$\boxed{\dot{C} = \sum_i \dot{x}_i = \sum_i x_i \left(\lambda_i + \sum_j \kappa_{ij}x_{j} \right) - C \phi = (1-C)\phi}$.

Clearly:

$\lim_{C \to 1} (1-C)\phi = 0$,

that is, this quick calculation shows that the total concentration $C$ remains constant.

Let us consider now the case of homogeneous interactions such that

$\kappa_{i \neq j} = \kappa$, $\kappa_{ii} = 0$, $\lambda_i = \alpha i$,

$\boxed{\dot{x}_{i} = x_{i} \left(\lambda_i + \kappa \sum_{j \neq i} x_{j} - \phi \right)}$,

which becomes

$\boxed{\dot{x}_i = x_i \left(\lambda_i + \kappa - \kappa x_i - \phi\right)}$.

This is a one-dimensional ODE with the following invariant submanifolds:

$\boxed{x_{i}^* = \frac{\lambda_i + \kappa - \phi}{\kappa}}$,

$\boxed{x_i^* = 0, \quad \lambda_i = N \alpha}$.

With homogeneous interactions, the concentrations with the largest growth rates will dominate, so there exists a $N^*$ such that $1 \leq N^* \leq N$ where

$\boxed{x_i^* = \frac{\lambda_i + \kappa - \phi}{\kappa}, \quad N^* \leq i \leq N}$,

$\boxed{0, \quad 1 \leq i < N^*}$.

The quantities $N^*$ and $\phi$ are determined via normalization conditions that give us a system of equations:

$\boxed{1 = \frac{\alpha}{2\kappa} \left[N(N+1) - N^*(N^* - 1)\right] + \left[\frac{\kappa - \phi}{\kappa}\right] \left(N + 1 - N^*\right)}$,

$\boxed{0 = \frac{\lambda_{N^*-1} + \kappa - \phi}{\kappa} = \frac{\alpha(N^* - 1)}{\kappa} + \frac{\kappa - \phi}{\kappa} }$.

For large $N, N^*$, we obtain the approximation

$\boxed{N - N^* \approx \sqrt{\frac{2 \kappa}{\alpha}}}$,

which is the number of surviving species.

Clearly, this is non-zero for a finite catalytic rate $\kappa$. This shows the formation of a hypercycle of molecules/quasispecies.

These computations clearly should be taken with a grain of salt. As pointed out in several sources, hypercycles describe closed systems, but, life exists in an open system driven by an energy flux. But, the interesting thing is, despite this, the very last calculation shows that there is clear division between molecules $i = N^*, \ldots N$ which can be considered as a type of primordial life-form separated by these molecules belonging to the environment.

## Sikhs in the Army

There has been much noise in recent days of Sikhs wanting to enlist in the U.S. Army and being unable to do so because they insist on following their religious mandates of uncut hair, an untrimmed beard, and covering their hair with a turban. The recent news stories are summarized here:

http://www.newsday.com/opinion/sikh-student-faces-the-army-s-catch-22-editorial-1.9627206

As usual, a myriad of folks have come out chiding the Sikh person for not conforming by disobeying his religion and removing his hair and beard. Such comments have been supported with questions that have typically come up whenever similar stories have come in the media of how Sikhs are expected to wear gas masks, how can they perform in combat operations without a helmet, etc… The point is that all of these issues are in fact, non-issues and are completely unfounded. There is much literature on Sikhs’ performance in the various wars throughout history and their success in said wars with turbans and beards, so I will not pursue that discussion here. However, I would like to take this opportunity to point out a level of hypocrisy  which people who oppose Sikhs in the military on the aforementioned grounds seem to have a penchant for. Here are just a few examples of countless numbers of White, American soldiers fighting in US conflicts with beards and in some cases, long hair. Why weren’t the same questions and objections raised in their cases?

Here are just some examples of Sikhs fighting and giving their lives in World War II for the Allied forces. As you can see, there are no technical issues of turbans and beard arising in these cases:

Winston Churchill had this to say about Sikhs as well:

“…..It is a matter of regret that due to the obsession of the present times people are distorting the superior religious and social values, but those who wish to preserve them with respect, we should appreciate them as well as help them. Sikhs do need our help for such a cause and we should give it happily. Those who know the Sikh history, know England’s relationship with the Sikhs and are aware of the achievements of the Sikhs, they should persistently support the idea of relaxation to Sikhs to ride a motorbike with their turbans on, because it is their religious privilege.”

“…British people are highly indebted and obliged to Sikhs for a long time. I know that within this century we needed their help twice and they did help us very well. As a result of their timely help, we are today able to live with honour, dignity, and independence. In the war, they fought and died for us, wearing the turbans. At that time we were not adamant that they should wear safety helmets because we knew that they are not going to wear them anyways and we would be deprived of their help. At that time due to our miserable and poor situation, we did not force it on them to wear safety helmets, why should we force it now? Rather, we should now respect their traditions and by granting this legitimate concession, win their applaud.”

So, we should all strive to be a bit more educated in this regard. These exemptions have been granted to White, American soldiers in the past, and even if not in a formal sense, there is an eerie silence coming from the same critics of Sikhs wanting to join the military when non-Sikhs have also not conformed to these rules as the above pictures clearly demonstrate.

## A Universe from Nothing

Many people have obviously been reading Lawrence Krauss’ infamous book: “A Universe from Nothing: Why There is something Rather Than Nothing”

Krauss and many other physicists continuously engage in this type of low-level philosophy with the ironic goal of diminishing the value of philosophy using “science”.

This paper dissects all the arguments in Krauss’ book and shows from a mathematical standpoint that like others who make similar arguments, they are not grounded in actual physics and are extremely flawed. One therefore concludes, that such arguments are not based in science, but in bad philosophy.

The paper: A Universe from Nothing

A teaser: This is what “nothing” actually looks like, well one depiction of it anyways:
But this is not nothing, it is something, where did this structure come from? Krauss actually ignores the question entirely in his book, which is very strange.

The famed cosmologist George Ellis also has discussed Krauss’ book in one of his talks, here is the link for that:

A video making some of the arguments in the above paper easier to understand can be found here:

## Sikhs and Diwali

For years now, I have heard this constant story of how it is acceptable for Sikhs to celebrate Diwali as per the Hindu traditions of lighting lamps, etc… Further, Raagis and Bhai Sahibs in Gurdwaras have conflated Bandhi Chorr Diwas with lighting lamps as per Hindu Diwali traditions. They further support these ideas with the supposed Vaar from Bhai Gurdas Jee, in which they ironically only mention and repeat the first line! : “deewaalee dee raath dheevae baaleean”. Of course, just by reading this line, it would suggest that the aforementioned actions are justified. But taking one line completely out of context leads one to these conclusions. A full reading of Bhai Gurdas Jee’s Vaar on the Diwali matter which given the timeframe is also a historical first-hand account suggests that Sikhs are to practice completely the opposite and in fact, lighting lamps is contrary to Gurmat. The full Vaar’s transliteration is below:

Vaars Bhai Gurdaas

diwali dee raath dheevae baaleeani
thaarae jaath sanaath a(n)bar bhaaleean
fulaa(n) dhee baagaath chun chun chaaleean
theerathh jaathee jaath nain nihaaleean
har cha(n)dhuree jhaath vasaae ouchaaleean
guramukh sukhafal dhaath shabadh samhaaleean

The essence of this Vaar is in every line after the first. Namely, in the third, fourth, and fifth lines, Bhai Gurdas Jee compares those that celebrate Diwali by lighting lamps akin to those who go on long pilgrimages to find God, and to those who search for God by worshipping the stars, or things in nature, etc… All contrary to Gurmat by a simple reading of Japjee Sahib! Indeed, Bhai Sahib Jee in the last line clearly states that a person of Gurmat does not practice any of these things, which he declares to be temporary and pointless.

So, there you have it. A simple reading of the full Vaar changes the entire context of the “importance” of Diwali in Sikhism. I doubt many Sikhs will read this posting with sincerity, but someone has to speak the truth!