On Relationship between X and Y chromosome evolution and PID control

First of all, I would like you to read my previous post on the graphical interpretation of the mechanisms of evolution of X and Y chromosomes.

These mechanisms clearly demonstrate the greater changeability of the X pool (in females) than the Y pool  (present only in males) – simply due to the fact that X chromosomes in females merge and branch (called fan in and fan out).

The next, in my opinion, interesting observation is drawn from the notions of mathematical analysis and dynamical systems theory. Here we have ideas of proportionality, integration, differentiation, on one hand, and notions of combinationality and sequentiality on the other.

If we look at the way how X-chromosomes evolve with fan-in mergers, we clearly see the features akin to proportionality and differentiality. The outgoing X pools are sensitive to the incoming X pools and their combinations. Any mixing node in this graph shows high sensitivity to inputs.

Contrary to that, the way of evolution of Y-chromosomes with NO fan-in contributions, clearly shows the elements of integration and sequentiality, or inertia, i.e. the preservation of the long term features.

So, the conclusions that can be drawn from this analysis are:

  1. Males tend to bring the integral or sequential (cf. sequential circuits in digital systems – with longer term memory) aspect to the overall process of evolution
  2. Females tend to bring the proportional/differential or combinatorial (cf. combinational circuits – with shorter term memory)
  3. The presence of both male and female genetics are essential for stability of the evolution and survival of the kind, much like the PID feedback control helps stability of dynamical systems, and much like the combination of combination and sequential circuits allow computer systems to operate according to their programs.

Again, I would be grateful for any comments and observations!

PS. By looking at the way how our society is now governed (cf. female or male presidents and prime ministers), you might think whether we are subject to differentiality/combinatorics or integrality/sequentiality and hence whether we are stable as a dynamical system or systems (in different countries).

Happy Days!

 

 

 

 

 

On the dynamics of evolution of Y and X chromosomes

It is a known fact that men inherit both Y and X chromosomes while women only X chromosomes.

As a corollary of that fact we also know that Y-chromosomes, sometimes synonymized with Y-DNA, are only inherited by the male part of the human race. This means that Y-chromosome inheritance mechanism is only forward-branching, i.e. Y-DNA is passed from one generation to the next generation “nearly” unchanged. As I am not an expert in genetics I cannot state precisely, in quantitative terms, what this “nearly” is worth. Suppose this “nearly” is close to 100% for simplicity.

Below is a diagram which illustrates my understanding of the mechanism of inheritance of Y-chromosomes.

This diagram is basically a branching tree, showing the pathways of the Y-DNA from one generation to the future generations of males. The characteristic feature of this inheritance mechanism is that it is Fan-out only. Namely, there is no way that the Y-DNA can be obtained by merging different Y-DNAs because we have no Fan-in mechanism.

Let’s now consider the mechanism of inheritance and evolution of X-chromosomes.The way how I see this mechanism is shown in the following diagram.

X-chromosomes are inherited by both males and females. But, as I understand, this happens in two different ways.

Each female takes a portion of X chromosomes from her father (let’s denote it as X1) and a portion of X chromosomes from her mother (denoted by X2), thereby producing its own set of chromosomes X2’ which is a function of X1 and X2. Similar inheritance is in the next generation where X2’’=f(X1’,X2’).

Each male, however, only inherits X chromosomes from his mother, as shown above, where X1’’=f(X2’).

At each generation, when the offspring produced has a female, there is a merge of X chromosomes from both parents. This means that the pool of X chromosomes as we go down the generations is constantly changed and renewed with new DNA from different incoming branches.

This mechanism is therefore both Fan-in and Fan-out. And this is not a tree but a directed acyclic graph.

What sort of conclusion can we draw from this analysis? Well, I draw many interesting (to me at least) conclusions associated with the dynamics of evolution of the genetic pool of males and females. One can clearly see that the dynamics of genesis of females is much higher than that of males. Basically, one half of a male’s genesis remains “nearly” (please note my earlier remark about “nearly”) unchanged, and only the other half is subject to mutation, whereas in females both halves are changed.

I can only guess that Y-chromosomes are probably affected by various factors such as geographical movements, difference in environment, deceases etc., but these mutations are nowhere near as powerful as the mergers in the X-pool.

In my next memo I will write about the relationship between the above mechanisms of evolution and PID (proportional-integrative-differential) control in dynamical systems, which will lead to some conjectures about the feedback control mechanisms in evolution of species.

I would be grateful if those whose knowledge of human genetics is credible enough could report to me of any errors in my interpretation of these mechanisms.

Newcastle’s Microsystems group (http://www.ncl.ac.uk/engineering/research/eee/microsystems/),

in collaboration with Newcastle’s Computing Science colleagues, as well as with the teams from Imperial College and Southampton Universities (under PRiME project – http://www.prime-project.org) , has published a visionary paper in IEEE Computer on how to analyse the interplay between performance, energy and reliability of computing systems with increasing number of processor cores.

Here is the video: https://www.computer.org/computer-magazine/2017/08/08/voltage-throughput-power-reliability-and-multicore-scaling/

And for some time it will be front page on the multimedia front page: https://www.computer.org/computer-magazine/category/multimedia/

Electromagnetic Compatibility event (EMC-COMPO’17) in St. Petersburg

A very interesting workshop was held in my Alma Mater (LETI – Electrotechnical Universrity) in Saint Petersburg, Russia on 4-8 July 2017.

https://emccompo2017.eltech.ru

The workshop contained lots of interesting presentations – largely from industry and largely on modelling and empirical measurements of the EM interference in microsystems and ICs. Basically, the problem of reuse and block replacement is huge due to the unpredictability of the EM effects between components on PCB and on chip.

Here are the presentations:

https://emccompo2017.eltech.ru/results/presentations

Milos Krstic (from IHP) and I gave a keynote talk, which consisted of two parts:

(1) Digital Systems Clocking with and without clock: a historical retrospective (emphasizing the role of researchers from LETI – mostly Victor Varshavsky’s group where I used to work in the 1980s)

http://www.eltech.ru/assets/files/en/emccompo-2017/presentations/25-Digital-Systems-Clocking-with-and-without-clock.pdf

(2) Main technical contribution: Reducing Switching Noise Effects by Advanced Clock Management: M. Krstic, X. Fan, M. Babic, E. Grass, T. Bjerregaard, A. Yakovlev

http://www.eltech.ru/assets/files/en/emccompo-2017/presentations/03-Reducing-Switching-Noise-Effects.pdf

 

Tutorial on EDA for Asynchronous Control for Analogue-Mixed-Signal

We gave a 3 hour tutorial at IEEE Int Conference on Electronics Circuits and Systems (ICECS’16) in Monaco on the 11th December 2016.

http://icecs.isep.fr/tutorial.html#tutorial7

The handout can be downloaded from here:

https://www.staff.ncl.ac.uk/alex.yakovlev/home.formal/talks/ICECS2016-Yakovlev-tutorial-handouts.pdf

We also organised a special session on Oscillator Based Computing:

http://www.epapers.org/icecs2016/ESR/session_view.php?session_id=9

where one of our papers was presented:

https://www.researchgate.net/publication/311667154_Stacking_Voltage-Controlled_Oscillators_Analysis_and_Application

 

 

Talking at the 2016 ARM Research Summit

Last week there was an inaugural ARM Research Summit.

https://developer.arm.com/research/summit

I gave a talk on Power & Compute Codesign for “Little Digital” Electronics.

Here are the slides of this talk:

https://www.staff.ncl.ac.uk/alex.yakovlev/home.formal/Power-and-Compute-Talk

Here is the abstract of my talk:

Power and Compute Codesign for “Little Digital” Electronics

Alex Yakovlev, Newcastle University

alex.yakovlev@ncl.ac.uk

The discipline of electronics and computing system design has traditionally separated power management (regulation, delivery, distribution) from data-processing (computation, storage, communication, user interface). Power control has always been a prerogative of power engineers who designed power supplies for loads that were typically defined in a relatively crude way.

 

In this talk, we take a different stance and address upcoming electronics systems (e.g. Internet of Things nodes) more holistically. Such systems are miniaturised to the level that both power management and data-processing are virtually inseparable in terms of their functionality and resources, and the latter are getting scarce. Increasingly, both elements share the same die, and the control of power supply, or what we call here a “little digital” organ, also shares the same silicon fabric as the power supply. At present, there are no systematic methods or tools for designing “little digital” that could ensure that it performs its duties correctly and efficiently.  The talk will explore the main issues involved in formulating the problem of and automating the design of little digital circuits, such as models of control circuits and the controlled plants, definition and description of control laws and optimisation criteria, characterisation of correctness and efficiency, and applications such as biomedical implants, IoT ‘things’ and WSN nodes.

 

Our particular focus in this talk will be on power-data convergence and ways of designing energy-modulated systems [1].  In such systems, the incoming flow of energy will largely determine the levels of switching activity, including data processing – this is fundamentally different from the conventional forms where the energy aspect simply acts as a cost function for optimal design or run-time performance.

 

We will soon be asking ourselves questions like these: For a given silicon area and given data processing functions, what is the best way to allocate silicon to power and computational elements? More specifically, for a given energy supply rate and given computation demands, which of the following system designs would be better? One that involves a capacitor network for storing energy, and investing energy into charging and discharging flying capacitors through computational electronics which would be able to sustain high fluctuations of the Vcc (e.g. built using self-timed circuit). The other one that involves a switched capacitor converter to supply power as a reasonably stable Vcc (could be a set of levels). In this latter case, it would be necessary also to invest some energy into powering control for the voltage regulator. In order to decide between these two organisations, one would need to carefully model both designs and characterise them in terms of energy utilisation and delivery of performance for the given computation demands. At present, there are no good ways for co-optimising power and computational electronics.

 

Research in this direction is in its infancy and this is only a tip of the iceberg. This talk will shed some light on how we are approaching the problem of power-data co-design at Newcastle, in a series of research projects producing novel types of sensors, ADCs, asynchronous controllers for power regulation, and software tools for designing “little digital” electronics.

[1] A. Yakovlev. Energy modulated computing. Proceedings of DATE, 2011, Grenoble,  doi: 10.1109/DATE.2011.5763216

My vision of Bio-inspired Electronic Design

I took part in a Panel on Bio-inspired Electronic Design Principles at the

Here are my slides

The quick summary of these ideas is here:

 

Summary of ideas for discussion from Alex Yakovlev, Newcastle University

 

With my 30 years of experience in designing and automating the design of self-timed (aka asynchronous) systems, I have been involved in studying and exploiting in practice the following characteristics of electronic systems:  inherent concurrency, event-driven and causality-based processing, parametric variation resilience, close-loop timing error avoidance and correction, energy-proportionality, digital and mixed-signal interfaces. More recently, I have been looking at new bio-inspired paradigms such as energy-modulated and power-adaptive computing, significance-driven approximate computing, real-power (to match real-time!) computing, computing with survival instincts, computing with central and peripheral powering and timing, power layering in systems architecting, exploiting burstiness and regularity of processing etc.

In most of these the central role belongs to the notion of energy flow as a key driving force in the new generation of microelectronics. I will therefore be approaching most of the Questions raised for the Panel from the energy flow perspective. The other strong aspect I want to address that acts as a drive for innovation in electronics is a combination of technological and economic factors, which is closely related to survival, both in the sense of longevity of a particular system as well as survival of design patterns and IPs as a longevity of the system as a kind or as a system design process.

My main tenets in this discussion are:

  • Compute where energy naturally flows.
  • Evolve (IPs, Designs) where biology (or nature as a whole) would evolve its parts (DNA, cells, cellular networks, organs).

I will also pose as one of the biggest challenges for semiconductor system the challenge of massive informational connectivity of parts at all levels of hierarchy, this is something that I hypothesize can only be addressed in hybrid cell-microelectronic systems. Information (and hence, data processing) flows should be commensurate to energy flows, only then we will be close to thermodynamic limits.

Alex Yakovlev

11.08.2016

 

Newcastle Asynchronous Workshop 2016

We have just hosted an extraordinary event here, including

Newcastle Concurrency Workshop:

http://www.ncl.ac.uk/eee/research/seminars/archivedevents/eventnewcastleconcurrencytheoryworkshop.html

Newcastle Asynchronous Workshop:

http://www.ncl.ac.uk/eee/research/seminars/archivedevents/eventnewcastleasynchronousworkshop.html

and

Newcastle Workcraft Tutorial:

http://www.ncl.ac.uk/eee/research/seminars/archivedevents/eventworkcrafttutorial.html

The main organisers of these workshops were Maciej Koutny, Andrey Mokhov and Danil Sokolov

The workshops attracted more than 30 external attendees and speakers.

Part of the Asynchronous Workshop was linked with a Festschrift event for my 60th birthday, where Andrey Mokhov gave me a special Festchrift volume edited by him and printed by Newcastle University publishing service. The book cosists of 30 essays written by 55 researchers from different parts of the world – they included my colleagues in the Async community, Newcastle colleagues, my former and current PhD students and some good friends and colleagues with many years of friendship and collaboration.

The book exists in electronic format and if someone wishes to have a copy, please contact Andrey Mokhov who will send you the pdf file.

At this workshop I gave a talk about the 25-year history of Asynchronous Research at Newcastle. Here are the slides of my talk:

This Asynchronous World-AlexY