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

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

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:

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
• 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:

“…..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

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!

Reply to Recent NYT Article: “God, Darwin, and My College Biology Class”

I recently came across the article/op-ed in the NYTimes, titled, “God, Darwin, and My College Biology Class”, http://www.nytimes.com/2014/09/28/opinion/sunday/god-darwin-and-my-college-biology-class.html?_r=0

In this article, it is stated: “Since Darwin, however, we have come to understand that an entirely natural and undirected process, namely random variation plus natural selection, contains all that is needed to generate extraordinary levels of non-randomness. Living things are indeed wonderfully complex, but altogether within the range of a statistically powerful, entirely mechanical phenomenon.”

When it is stated that “contains all that is needed to generate extraordinary levels of non-randomness” is factually not accurate, for one is making the mistake that many reductionists make by assuming that all complexity arises from bottom-up causation alone, and are completely ignoring the effects of top-down causation. The reason is as follows: Lower levels of complexity are necessarily governed by uncertainties due to quantum mechanics, it is not clear how these quantum uncertainties transition to a classical state. Mathematically, these uncertainties that are at the heart of the random variation that is cited are governed in a Hilbert, L^2 Lebesgue integrable space. Classical systems, determined by phase space manifolds have these probabilistic domains in the cotangent bundle of the manifold. The article is essentially saying that the cotangent bundle determines the phase space and not the other way around which is not correct. Further, there remains the unsolved issue of how the quantum fluctuations become classical (unless you follow the untestable many worlds route, which has major problems – see S D Hsu Modern Physics Letters A27: 1230114 (2012) for one interesting comment, and the writings of Sudarsky.

On the other side, top-down causation via cosmology and Einstein’s equations seed the correct conditions for dynamical Darwinian evolution to take place to begin with, for some reason, the author completely leaves this out.

Without a question, the author is an expert an evolutionary biology, but I am afraid he has looked through these issues through a very narrow lens, which does not do the issue a full and complete justification, and indeed, is responsible for much of the discomfort with evolutionary theory that is described so accurately and well in the article.

In the mean time, I would humbly suggest that the interested reader look at the following articles which describe Darwinian evolution in a more complete context as a function of emergence and complexity through physics which underlies biology. Also, one should see the work of Denis Noble, http://musicoflife.co.uk who advocates for a dynamical systems-based view of biological systems, which I personally believe to be correct, as it is much more mathematically and physically sound compared to standard evolutionary theory. This YouTube video of a lecture from the noted cosmologist GFR Ellis also sums up the problem with the reductionist view of evolutionary biology: http://youtu.be/nEhTkF3eG8Q

Title:
Laws, Causation and Dynamics at Different Levels
Authors:
Butterfield, Jeremy
Publication:
eprint arXiv:1406.4732
Publication Date:
06/2014
Origin:
ARXIV
Keywords:
Physics – History and Philosophy of Physics, Physics – Popular Physics
Comment:
29 pages, 3 figures; Interface Focus (Royal Society London), volume 2, 2012, pp. 101-114; doi:10.1098/rsfs.2011.0052
Bibliographic Code:
2014arXiv1406.4732B
Abstract

I have two main aims. The first is general, and more philosophical (Section 2). The second is specific, and more closely related to physics (Sections 3 and 4). The first aim is to state my general views about laws and causation at different ‘levels’. The main task is to understand how the higher levels sustain notions of law and causation that ‘ride free’ of reductions to the lower level or levels. I endeavour to relate my views to those of other symposiasts. The second aim is to give a framework for describing dynamics at different levels, emphasising how the various levels’ dynamics can mesh or fail to mesh. This framework is essentially that of elementary dynamical systems theory. The main idea will be, for simplicity, to work with just two levels, dubbed ‘micro’ and ‘macro’ which are related by coarse-graining. I use this framework to describe, in part, the first four of Ellis’ five types of top-down causation.

Title:
The arrow of time and the nature of spacetime
Authors:
Ellis, George F R
Publication:
eprint arXiv:1302.7291
Publication Date:
02/2013
Origin:
ARXIV
Keywords:
General Relativity and Quantum Cosmology, Physics – History and Philosophy of Physics
Comment:
56 pages, 7 figures
Bibliographic Code:
2013arXiv1302.7291E
Abstract

This paper extends the work of a previous paper [arXiv:1208.2611] on the flow of time, to consider the origin of the arrow of time. It proposes that a past condition’ cascades down from cosmological to micro scales, being realized in many microstructures and setting the arrow of time at the quantum level by top-down causation. This physics arrow of time then propagates up, through underlying emergence of higher level structures, to geology, astronomy, engineering, and biology. The appropriate space-time picture to view all this is an emergent block universe (EBU’), that recognizes the way the present is different from both the past and the future. This essential difference is the ultimate reason the arrow of time has to be the way it is.

Title:
Recognising Top-Down Causation
Authors:
Ellis, George F R
Publication:
eprint arXiv:1212.2275
Publication Date:
12/2012
Origin:
ARXIV
Keywords:
Physics – Classical Physics, Nonlinear Sciences – Adaptation and Self-Organizing Systems, Physics – History and Philosophy of Physics
Comment:
11 pages, 2 figures, 2 tables. 2nd prize in FQXI essay competition
Bibliographic Code:
2012arXiv1212.2275E
Abstract

One of the basic assumptions implicit in the way physics is usually done is that all causation flows in a bottom up fashion, from micro to macro scales. However this is wrong in many cases in biology, and in particular in the way the brain functions. Here I make the case that it is also wrong in the case of digital computers – the paradigm of mechanistic algorithmic causation – and in many cases in physics, ranging from the origin of the arrow of time to the process of state vector preparation. I consider some examples from classical physics, as well as the case of digital computers, and then explain why this is possible without contradicting the causal powers of the underlying microphysics. Understanding the emergence of genuine complexity out of the underlying physics depends on recognising this kind of causation.

Title:
Evolutionary Transitions and Top-Down Causation
Authors:
Imari Walker, Sara; Cisneros, Luis; Davies, Paul C. W.
Publication:
eprint arXiv:1207.4808
Publication Date:
07/2012
Origin:
ARXIV
Keywords:
Nonlinear Sciences – Adaptation and Self-Organizing Systems, Quantitative Biology – Other Quantitative Biology
Comment:
8 pages, 4 figures; Proceedings of Artificial Life XIII (2012) p. 283-290
Bibliographic Code:
2012arXiv1207.4808I
Abstract

Top-down causation has been suggested to occur at all scales of biological organization as a mechanism for explaining the hierarchy of structure and causation in living systems. Here we propose that a transition from bottom-up to top-down causation — mediated by a reversal in the flow of information from lower to higher levels of organization, to that from higher to lower levels of organization — is a driving force for most major evolutionary transitions. We suggest that many major evolutionary transitions might therefore be marked by a transition in causal structure. We use logistic growth as a toy model for demonstrating how such a transition can drive the emergence of collective behavior in replicative systems. We then outline how this scenario may have played out in those major evolutionary transitions in which new, higher levels of organization emerged, and propose possible methods via which our hypothesis might be tested.

Title:
On the limits of quantum theory: Contextuality and the quantum-classical cut
Authors:
Ellis, George F. R.
Affiliation:
AA(Mathematics Department, University of Cape Town, South Africa)
Publication:
Annals of Physics, Volume 327, Issue 7, p. 1890-1932.
Publication Date:
07/2012
Origin:
ELSEVIER
(c) 2012 Elsevier Inc.
DOI:
10.1016/j.aop.2012.05.002
Bibliographic Code:
2012AnPhy.327.1890E
Abstract

This paper is based on four assumptions: 1. Physical reality is made of linearly behaving components combined in non-linear ways. 2. Higher level behaviour emerges from this lower level structure. 3. The way the lower level elements behaves depends on the context in which they are embedded. 4. Quantum theory applies to the lower level entities. An implication is that higher level effective laws, based on the outcomes of non-linear combinations of lower level linear interactions, will generically not be unitary; hence the applicability of quantum theory at higher levels is strictly limited. This leads to the view that both state vector preparation and the quantum measurement process are crucially based on top-down causal effects, and helps provide criteria for the Heisenberg cut that challenge some views on Schrödinger’s cat.

Title:
Top-Down Causation and Autonomy in Complex Systems
Authors:
Juarrero, Alicia
Affiliation:
AA(Emeritus, Prince George’s Community College)
Publication:
Downward Causation and the Neurobiology of Free Will, Understanding Complex Systems. ISBN 978-3-642-03204-2. Springer Berlin Heidelberg, 2009, p. 83
Publication Date:
00/2009
Origin:
SPRINGER
Keywords:
Physics
(c) 2009: Springer Berlin Heidelberg
DOI:
10.1007/978-3-642-03205-9_5
Bibliographic Code:
2009dcnf.book…83J
Abstract

Evolutionary evidence shows that complex dynamical systems become increasingly self-directed and decoupled from merely energetic forces over time. In this paper I analyze these transformations, concentrating on changes in the type of top-down causation that characterizes such self-organized and autopoietic pro cesses. Specifically, I show that the top-down selection criteria of these systems makes some of them autonomous, and that because once evolution reaches humans the criteria according to which voluntary actions are selected are semantic and symbolic – and can be self-consciously chosen – human self-direction constitutes a form of strong autonomy that can arguably be considered “free will.”

Title:
Top-Down Causation and the Human Brain
Authors:
Ellis, George F. R.
Affiliation:
AA(Mathematics Department, University of Cape Town)
Publication:
Downward Causation and the Neurobiology of Free Will, Understanding Complex Systems. ISBN 978-3-642-03204-2. Springer Berlin Heidelberg, 2009, p. 63
Publication Date:
00/2009
Origin:
SPRINGER
Keywords:
Physics
(c) 2009: Springer Berlin Heidelberg
DOI:
10.1007/978-3-642-03205-9_4
Bibliographic Code:
2009dcnf.book…63E
Abstract

A reliable understanding of the nature of causation is the core feature of science. In this paper the concept of top-down causation in the hierarchy of structure and causation is examined in depth. Five different classes of top-down causation are identified and illustrated with real-world examples. They are (1) al gorithmic top-down causation; (2) top-down causation via nonadaptive information control; (3) top-down causation via adaptive selection; (4) top-down causation via adaptive information control; and (5) intelligent top-down causation (i.e., the effect of the human mind on the physical world). Recognizing these forms of causation implies that other kinds of causes than physical and chemical interactions are effective in the real world. Because of the existence of random processes at the bottom, there is sufficient causal slack at the physical level to allow all these kinds of causation to occur without violation of physical causation. That they do indeed occur is indicated by many kinds of evidence. Each such kind of causation takes place in particular in the human brain, as is indicated by specific examples.

Title:
Top-Down Causation by Information Control: From a Philosophical Problem to a Scientific Research Program
Authors:
Auletta, G.; Ellis, G. F. R.; Jaeger, L.
Publication:
eprint arXiv:0710.4235
Publication Date:
10/2007
Origin:
ARXIV
Keywords:
Quantitative Biology – Other Quantitative Biology
Comment:
Revised version to meet referee’s comments, and responding to a paper by Wegscheid et al that was not mentioned in the previous version. 23 pages, 9 figures
Bibliographic Code:
2007arXiv0710.4235A
Abstract

It has been claimed that different types of causes must be considered in biological systems, including top-down as well as same-level and bottom-up causation, thus enabling the top levels to be causally efficacious in their own right. To clarify this issue, important distinctions between information and signs are introduced here and the concepts of information control and functional equivalence classes in those systems are rigorously defined and used to characterise when top down causation by feedback control happens, in a way that is testable. The causally significant elements we consider are equivalence classes of lower level processes, realised in biological systems through different operations having the same outcome within the context of information control and networks.

Title:
Physics and the Real World
Authors:
Ellis, George F. R.
Affiliation:
AA(Mathematics Department, University of Cape Town)
Publication:
Foundations of Physics, Volume 36, Issue 2, pp.227-262
Publication Date:
02/2006
Origin:
CROSSREF; SPRINGER
Keywords:
Physics, emergence, causality
DOI:
10.1007/s10701-005-9016-x
Bibliographic Code:
2006FoPh…36..227E
Abstract

Physics and chemistry underlie the nature of all the world around us, including human brains. Consequently some suggest that in causal terms, physics is all there is. However, we live in an environment dominated by objects embodying the outcomes of intentional design (buildings, computers, teaspoons). The present day subject of physics has nothing to say about the intentionality resulting in existence of such objects, even though this intentionality is clearly causally effective. This paper examines the claim that the underlying physics uniquely causally determines what happens, even though we cannot predict the outcome. It suggests that what occurs is the contextual emergence of complexity: the higher levels in the hierarchy of complexity have autonomous causal powers, functionally independent of lower level processes. This is possible because top-down causation takes place as well as bottom-up action, with higher level contexts determining the outcome of lower level functioning and even modifying the nature of lower level constituents. Stored information plays a key role, resulting in non-linear dynamics that is non-local in space and time. Brain functioning is causally affected by abstractions such as the value of money and the theory of the laser. These are realised as brain states in individuals, but are not equivalent to them. Consequently physics per se cannot causally determine the outcome of human creativity, rather it creates the possibility space allowing human intelligence to function autonomously. The challenge to physics is to develop a realistic description of causality in truly complex hierarchical structures, with top-down causation and memory effects allowing autonomous higher levels of order to emerge with genuine causal powers.

Title:
Emergence and Dissolvence in the Self-organisation of Complex Systems
Authors:
Testa, Bernard; Kier, Lemont B.
Publication:
Entropy, vol. 2, Issue 1, p.1-25
Publication Date:
03/2000
Origin: