Monday 31 January 2022

A Matter of Sound

 ... is the title (in its print edition) of an article in the January 2022 issue of Physics World, the magazine of the UK Institute of Physics. It appears on the Physics World website under the title Sonifying science: from an amino acid scale to a spider silk symphony.

The notion underlying the article is that vibrations or movements at molecular levels can be represented as sounds and, therefore, in the form of music. And, equally, vice versa - a musical form can be used to predict a structure at a molecular level. The main substance of the article applies this notion to the amino acid structure of the proteins that occur in living things.

...we developed a systematic way of translating a protein’s sequence of amino acids into a musical sequence, using the physical properties of the molecules to determine the sounds (ACS Nano 13 7471). The system translates the 20 types of amino acids (figure 1) into a 20-tone scale. Any protein’s long sequence of amino acids then becomes a sequence of notes. The sounds are transposed in order to bring them within the audible range for humans (20 Hz–20 kHz), without affecting the structural features by following the concept of transpositional equivalence. Indeed, the tones and their relationships are based on the actual vibrational frequencies of each amino acid molecule itself, providing a physical basis for protein sonification.

It is worth listening to the "amino acid scale" embedded in the original online article. It is impressively musical to the ear, though we would not recognise it as a scale in the conventional sense. The musical representation of the Lysozyme enzyme, also embedded in the article, is considerably less pleasing to the ear.

It would be very easy to make more of this idea in philosophical terms than the idea itself really justifies. Nevertheless, it is interesting to reflect on the suggestion that the structure and behaviour of key molecules that make up living things can be understood in a form of music, albeit a form that noticeably differs from our usual understanding to musical form (for example, it being based on a 20-tone scale rather than a 12-tone scale). It suggests an aesthetic form that might be seen in those molecules, and in the life based upon them, something that a classical metaphysics would denote by the term "beauty". Whether or not the specific musical form suggested by the authors of this article proves to withstand the scrutiny over time of scientific peers, there remains the suggestion implied in it that the molecules at the heart of living things are capable of being represented by an aesthetic form.

A couple of further points. Whilst each amino acid in a protein is represented by its own tone, the higher order structure of the protein - its folding and the sequencing of different amino acids in the chain of the protein - are expressed as rhythm and note volume. The musical representation is therefore, in principle, able to express increasing complexity in protein molecules.

The article also refers to work done on different coronaviruses, including the virus causing the current COVID-19 pandemic. We have heard much about the "spike protein" of this virus, and the way in which it binds to a receptor in our human cells, leading to the infection of the cell by the virus and the subsequent reproduction of the virus. 

Previously, researchers looked at biochemical mechanisms when studying how spike proteins, which give coronaviruses their distinct crown-like appearance, interact with human cells. Instead, we used atomistic simulations and AI to study the mechanical aspects of how the spike proteins move, change shape and vibrate.

The authors of the article were able to establish a correlation between how infectious and dangerous a virus might be and two particular features of the vibrational motions of the spike protein molecules in coronaviruses. This offers a potential technique for quickly screening emerging virus variants to assess their potential risks; and the possibility of treating coronaviruses by finding a molecule that will bind on to the spike proteins so that their vibrations are limited or cancelled out altogether.

Wednesday 19 January 2022

Unnecessary burdens

 I found this post at Where Peter Is a thoughtful read: They Lay Heavy Burdens on the Shoulders of Others. I think it usefully indicates the consequences that can be experienced as a result of the existence of a kind of "alternative teaching authority" alongside that of the established hierarchy of the Church. It also gives a suggestion, in its use of the term "reactionary", of the possible merging of a (conservative) political stance with a Traditionalist ecclesial stance. 

What I think is most useful in the post is its account of how the activity of the proponents of this alternative teaching impacts on ordinary people who follow them, and in ways that are quite unnecessary. Very often we are looking at situations that are matters of prudential choice and not religious imperative, as, for example, with the question of home schooling.

I am a little unsure of the suggestion that the need to keep a job constitutes a "grave reason" in terms of allowing the taking of a COVID-19 vaccine:

Since the Church has spoken, they should be free to receive a vaccine, if only to keep their jobs. In my opinion, this could be considered a “grave reason,” particularly when a job is necessary to support the family.

Since the Church's teaching on the matter has been made clear, certainly Catholics should feel free to receive a vaccine in order to keep their job and support their family , without any concern that they are taking part in an immoral action. But in another context, the need to support a family would not justify taking part in something that is taught by the Church as being morally unlawful. Hence, my hesitations here.

I have more difficulty with some of what the writer says about Amoris Laetitia, most particularly this sentence:

Pope Francis taught that under some circumstances, divorced and remarried Catholics can be admitted to Communion.

I think it is more accurate to say that Pope Francis allowed a possibility in the well known footnote in Amoris Laetitia. This possibility, however, is only a part of a wider programme of how the Church should help those in irregular marriage situations to grow in the life of grace and charity (cf the very sentence in n.305 to which the footnote is applied). I think the writer also misses the point that it is the manifest (ie publicly visible) and persistent (ie a public situation that may not change in the immediate moment) that leads to a canonical ruling that remarried people cannot receive the Sacraments of Penance and the Eucharist. 

I see three fundamental aspects to Pope Francis' teaching in Chapter 8 of Amoris Laetitia

Firstly, a recognition that a person living in an objective state of sin through an irregular marriage situation may be living to an extent a life of grace, and that they can grow in that life of grace (cf n.305). The post on Where Peter Is recognises this in a slightly different way in its account of mortal sin.

Secondly, there is a key place in the discernment of a particular situation for an examination of conscience, and the suggested path of this examination of conscience does involve "humility, discretion and love for the Church and her teaching" (cf. n.300). This examination of conscience is not a soft touch if the pattern suggested by Pope Francis is followed.

Thirdly, the key focus of the discernment is not that of reception or not of the sacraments but of how a person might engage with the Church's mission of charity in order to thereby grow in the life of grace. This is strongly argued in Amoris Laetitia n.306, and followed up by Pope Francis' observation in n.309 that it is providential that the Apostolic Exhortation is wirtten during the Year of Mercy, when the renewed practice of the works of charity was proposed to the Church. 

In other respects, though, I think the post at Where Peter Is has usefully given an account of the experience that can result from the unhelpful activity of some clerics and commentators.

Wednesday 12 January 2022

Synodality: the Legion of Mary as a model?

I am not sure I completely understand the UK's system of public honours, but each time a list of awards is published (typically, the New Years Honours and the Queen's Birthday Honours) I am reminded of the practice of the Legion of Mary, which is that no honours or presents are to be given to members. Instead, when there is some occasion that calls for recognition, a spiritual bouquet (ie a promise of prayers) is offered instead (cf p.303 of my edition of the Legion Handbook). 

In this, as in other things, Frank Duff seems to have been very much ahead of his time. Which prompted me to wonder whether he was also ahead of his time as far as "synodality" was concerned... 

The Legion Handbook (pp.11-12 in my edition) states the object of the Legion as follows - I have added the italics to draw attention to the aspect of "walking together" that is contained in this statement. The dimensions of ecclesial communion, participation and mission are also very apparent.

The object of the Legion of Mary is the glory of God through the holiness of its members developed by prayer and active co-operation, under ecclesiastical guidance, in Mary’s and the Church’s work of crushing the head of the serpent and advancing the reign of Christ. Subject to the approval of the Concilium, and to the restrictions specified in the official handbook of the Legion, the Legion of Mary is at the disposal of the bishop of the diocese and the parish priest for any and every form of social service and Catholic action which these authorities may deem suitable to the legionaries and useful for the welfare of the Church. Legionaries will never engage in any of these services whatsoever in a parish without the sanction of the parish priest or of the Ordinary.

The aspect of "walking together" is most clearly lived out when the (parish) priest spiritual director takes an active interest in the work of a praesidium, attending the weekly meetings and indicating work that might be undertaken. The structure of Legion councils also indicates the dimension of ecclesial communion - the praesidium is part of a Curia; Curiae are part of a Comitium; a Comitium comes under a Regia; and, finally, there is the international governing body of the Concilium. But at each level the role  a spiritual director indicates the "walking together" of the lay legionaries and the ordained ministry.

Participation and mission are reflected in the duty of legionaries to attend a weekly meeting and complete a weekly obligation of a substantive apostolic work (cf pp.191-194 of the Handbook). A key theme, both in the Legion Handbook and in the writings of Frank Duff is that of the necessity of a laity imbued with a vivid apostolic spirit, who work in collaboration with their clergy for the good of Church's mission. 

Is this perhaps the key to Pope Francis' encouragement that we should "walk together" on the synodal pathway?

Monday 10 January 2022

Pope Francis' address to the Diplomatic Corps: January 2022

 This is a very wide ranging address, and reflects, I think, not just the range of Pope Francis' engagement with the international and political sphere, but the range of such engagement that is typical of the Holy See in general. At the same time, however, it does include some articulations typical of Pope Francis. The full text is at the Vatican website: here. In the extracts below, the italics are all mine, and do not appear in the original text. As I usually do, I recommend reading the whole.

On the COVID-19 pandemic, Pope Francis situates his remarks about vaccination in the context of the obligations of the individual with regard to both their own health and the health of others:

It is therefore important to continue the effort to immunize the general population as much as possible. This calls for a manifold commitment on the personal, political and international levels. First, on the personal level. Each of us has a responsibility to care for ourself and our health, and this translates into respect for the health of those around us. Health care is a moral obligation. Sadly, we are finding increasingly that we live in a world of strong ideological divides. Frequently people let themselves be influenced by the ideology of the moment, often bolstered by baseless information or poorly documented facts. Every ideological statement severs the bond of human reason with the objective reality of things. The pandemic, on the other hand, urges us to adopt a sort of “reality therapy” that makes us confront the problem head on and adopt suitable remedies to resolve it. Vaccines are not a magical means of healing, yet surely they represent, in addition to other treatments that need to be developed, the most reasonable solution for the prevention of the disease.

On "ideological colonisation" on the part of international organisations:

The diminished effectiveness of many international organizations is also due to their members entertaining differing visions of the ends they wish to pursue. Not infrequently, the centre of interest has shifted to matters that by their divisive nature do not strictly belong to the aims of the organization. As a result, agendas are increasingly dictated by a mindset that rejects the natural foundations of humanity and the cultural roots that constitute the identity of many peoples. As I have stated on other occasions, I consider this a form of ideological colonization, one that leaves no room for freedom of expression and is now taking the form of the “cancel culture” invading many circles and public institutions. Under the guise of defending diversity, it ends up cancelling all sense of identity, with the risk of silencing positions that defend a respectful and balanced understanding of various sensibilities. A kind of dangerous “one-track thinking” [pensée unique] is taking shape, one constrained to deny history or, worse yet, to rewrite it in terms of present-day categories, whereas any historical situation must be interpreted in the light of a hermeneutics of that particular time, not that of today. 

The existence of enduring values:

Nor should we overlook “the existence of certain enduring values”. Those are not always easy to discern, but their acceptance “makes for a robust and solid social ethics. Once those fundamental values are adopted through dialogue and consensus, we realize that they rise above consensus”. Here I wish to mention in particular the right to life, from conception to its natural end, and the right to religious freedom.

 Commenting on the failure of the international community to resolve several long lasting conflicts in different nations, and the arms trade:

Dialogue and fraternity are two essential focal points in our efforts to overcome the crisis of the present moment. Yet “despite numerous efforts aimed at constructive dialogue between nations, the deafening noise of war and conflict is intensifying”.The entire international community must address the urgent need to find solutions to endless conflicts that at times appear as true proxy wars.....
Naturally, these conflicts are exacerbated by the abundance of weapons on hand and the unscrupulousness of those who make every effort to supply them. At times, we deceive ourselves into thinking that these weapons serve to dissuade potential aggressors. History and, sadly, even daily news reports, make it clear that this is not the case. Those who possess weapons will eventually use them, since as Saint Paul VI observed, “a person cannot love with offensive weapons in his hands”. Furthermore, “When we yield to the logic of arms and distance ourselves from the practice of dialogue, we forget to our detriment that, even before causing victims and ruination, weapons can create nightmares”. Today these concerns have become even more real, if we consider the availability and employment of autonomous weapon systems that can have terrible and unforeseen consequences, and should be subject to the responsibility of the international community.

 On the dignity of labour:

The second thing that I would like to mention briefly is labour, “an indispensable factor in building and keeping peace. Labour is an expression of ourselves and our gifts, but also of our commitment, self-investment and cooperation with others, since we always work with or for someone else. Seen in this clearly social perspective, the workplace enables us to learn to make our contribution towards a more habitable and beautiful world”. ....

In this context [ie the COVID-19 pandemic], we see even more clearly the importance of labour, since economic development cannot exist without it, nor can it be thought that modern technology can replace the surplus value of human labour. Human labour provides an opportunity for the discovery of our personal dignity, for encounter with others and for human growth; it is a privileged means whereby each person participates actively in the common good and offers a concrete contribution to peace. Here too, greater cooperation is needed among all actors on the local, national, regional and global levels, especially in the short term, given the challenges posed by the desired ecological conversion. The coming years will be a time of opportunity for developing new services and enterprises, adapting existing ones, increasing access to dignified work and devising new means of ensuring respect for human rights and adequate levels of remuneration and social protection.

Thursday 6 January 2022

Pope Francis on fatherhood and motherhood in today's society (and, incidentally, on pets and children)

 The news media have picked up on an observation made by Pope Francis during his General Audience address yesterday, referring to the way in which some couples seem to preference taking pets into their household rather than having children. The BBC News website, for example, headlines their report Pope Francis says choosing pets over kids is selfish. As is usual in these situations, it is worth looking at the whole of what was said, both to gain a context for the headlined remark and to discover if there is a more significant underlying message that Pope Francis was trying to communicate.

The remarks were made during a reflection on the role of St Joseph as the (foster) father of Jesus at the General Audience of 5th January 2022. Pope Francis opened his reflection with a short account of the Scriptural/theological context of St Joseph's fatherhood, relating it particularly to a Jewish practice according to which a brother of the deceased would marry a childless widow, the children of this new union having the deceased brother as their legal father and the brother being a kind of foster father (cf Deuteronomy 25:5-6). 

Joseph already knows that, for Mary’s son, a name had already been prepared by God – Jesus’ name is given to him by his true father, God – “Jesus”, which means “the Lord saves”; as the Angel explains, “He will save his people from their sins” (Mt 1:21). This particular aspect of Joseph now enables us to reflect on fatherhood and motherhood. And this, I believe, is very important: thinking about fatherhood today. Because we live in an age of notorious orphanhood, don’t we? It is curious: our civilization is something of an orphan, and this orphanhood can be felt. May Saint Joseph, who took the place of the real father, God, help us to understand how to resolve this sense of orphanhood that is so harmful to us today.

In his address, Pope Francis does not go on to further develop this idea that our civilisation today has an experience of being orphaned; but there is a theme here that would be worth exploring more deeply. Instead be goes on to speak about the nature of fatherhood and motherhood.

It is not enough to bring a child into the world to also be the child’s father or mother. “Fathers are not born, but made[in the Italian this reads "si diventa", which has more of sense of "becomes"]. A man does not become a father simply by bringing a child into the world, but by taking up the responsibility to care for that child. Whenever a man accepts responsibility for the life of another, in some way he becomes a father to that person” (Apostolic Letter Patris corde). I think in a particular way of all those who are open to welcome life by way of adoption, which is such a generous and beautiful, good attitude. Joseph shows us that this type of bond is not secondary; it is not an afterthought, no. This kind of choice is among the highest forms of love, and of fatherhood and motherhood.

Again, there is a thought here that is worthy of a more extended consideration. Is Pope Francis suggesting that adoptive parenthood is not to be seen as second-best to natural parenthood, but rather that it has, with St Joseph as in some way its archetype, an original dignity alongside that of natural parenthood? 

Pope Francis' remark about couples perhaps preferring owning pets over having children is part of a wider observation about the unwillingness of many couples today to have children, or to limit their families to one child only.

... this denial of fatherhood or motherhood diminishes us, it takes away our humanity. And in this way civilization becomes aged and without humanity, because it loses the richness of fatherhood and motherhood. And our homeland suffers, as it does not have children, and, as it has been said somewhat humorously, “and now who will pay the taxes for my pension, if there are no children?”: with laughter, but it is the truth. Who will take care of me? I ask of Saint Joseph the grace to awaken consciences and to think about this: about having children. Fatherhood and motherhood are the fullness of the life of a person. Think about this. It is true, there is the spiritual fatherhood of those who consecrated themselves to God, and spiritual motherhood; but those who live in the world and get married, think about having children, of giving life, which they will take from you for the future [the Italian here reads ... "deve pensare ad avere figli, a dare la vita, perché saranno loro che gli chiuderanno gli occhi, che penseranno al suo futuro"..." must think to have children, to give life, because it will be they who will close your eyes, who will think about your future"]. And also, if you cannot have children, think about adoption. It is a risk, yes: having a child is always a risk, either naturally or by adoption. But it is riskier not to have them. It is riskier to deny fatherhood, or to deny motherhood, be it real or spiritual. But denial, a man or woman who do not develop the sense of fatherhood or motherhood, they are lacking something, something fundamental, something important.

Here it is the thought that "motherhood and fatherhood are the fullness of the life of a person" that perhaps needs further exploration, particularly in the consideration of those who remain single and do not marry; and the idea of a societal experience of fatherhood and motherhood that is denied when couples do not favour having children.

There is rather more to discuss from this General Audience address than just the remark about pets and children!