Don’t Count your children until they’ve had the Pox: Weekly Series Intro & Part One.





They’ve had


P O X!




M.B. O’Hare



Contact DiG-Press via email for more information:

© M. B. O’ Hare. 2018.

May be used for educational purposes without written permission but with a citation and copyright notice linked to this source.



 Can We Now Count Our Children?

Whatever happened to the Great Plague of the middle ages; a disease we never had any medical interventions for? Although, back in the day, protection was adopted by visiting doctors who attended the sick – the mask with the beak of a bird was filled with various herb potions and if the afflicted didn’t die from the plague, surely they would have died of fright at the sight of such a vision on one’s sick bed.


Fig. 1: Physician attire for protection from the Black Death by Paul Fürst; Source: (CC-BY), commons.wikimedia. Vaccine added by author.

Now imagine what would happen if the old Plague in its true original colours (the same genes as the original Plague) returned to our modern communities today? Would we begin to die in our millions, or a third of Ireland’s population and the same proportion in Europe be wiped out as before? And bear in mind that as it turns out,  black rats and their fleas may be innocent after all! Therefore, no amount of avoiding them, or cleaning up rat-infested cesspits, would limit the spread of the Plague to-day.


Fig. 2: Rats may be innocent after all! Designed by the author.

As it happens, we don’t need to panic as the actual same Plague that once killed millions has already escaped out into the public at large on a number of occasions not that long ago. And in one unusually fatal case, it not only killed a pet (it is usually cats that get it – but it is still very rare indeed), but it also killed its owner – who unwittingly spread it to the broader community including unsuspecting infants in a day-care centre where she worked and they didn’t even show as much as a sniffle.

Interestingly, as the Plague itself hasn’t changed over the past half a millennia or so, we now find that having something like Chickenpox or Cold sores may actually have a lot to do with why we aren’t currently dying in our millions in more modern times.

Similarly, we could ask: What if Smallpox returned in its old colours? We don’t even have a vaccine any more to protect us! You may remember hearing of the threat of bioterrorist attacks being imminent in the early 2000s, and efforts were made to produce safe and effective vaccines, with rather mixed results on both counts? Again,  as it turns out – there may not be a need for panic as some of the most virulent strains have already escaped – quite by accident – into the public arena. These all originated from several labs and again, the impact was surprisingly minor.

All in all, it looks like we may have become generationally and naturally, immune to these once significantly more deadly pathogens – the Plague and Smallpox. Now we don’t have detailed and accurate mortality data  for the former disease due to it being so old, but we do have such data for the latter disease from London and this is compared to Ireland where official records only began in 1864 – the year after compulsory vaccination was introduced here and elsewhere as seen below:

smallpox London and Ireland compared

Fig. 3: Reproduced from Fig. 5.4. Deaths from smallpox per 1000 deaths from all causes in London, from 1629 to 1900. (Data from Guy (1882) and the Registrar General’s Statistical Review of England and Wales.) in F. Fenner, D. A. Henderson, I. Arita, Z. Jezek, I. D. Ladnyi (1988) – Smallpox and its Eradication. World Health Organization (WHO) 1988. Online here at the WHO website with Irish original data superimposed.   F. Fenner, D. A. Henderson, I. Arita, Z. Jezek, I. D. Ladnyi (1988) – Smallpox and its Eradication. World Health Organization (WHO) 1988. Online here at the WHO website. Irish graph superimposed number of annual deaths since records began in 1864, one year after compulsory vaccination – significantly scaled down to make a comparison with London data. Data derived from “Annual Reports on Marriages, Births and Deaths in Ireland, from 1864 to 2000” courtesy of An Phríomh-Oifig Staidrimh, Central Statics Office CSO, link.

As you can see from the above graphs, and indeed, clearly illustrated repeatedly throughout this study using graphs and historical sources, when we combine this with our more recent insights into natural generational immunity, we begin to understand how Nature works in much more sophisticated and mysteriously molecular ways than we have hitherto appreciated.

For instance, our history books describe in terrifying detail what can happen when an isolated indigenous community was initially devastated when they had first encountered some foreign and unfamiliar pathogens. Interestingly, these isolated populations were some of the healthiest and fittest individuals and naturally pristine natives.

However, this phenomenon has been studied in more recent times and we can now see that the relatively rapid recovery – over a few generations from such an event – cannot be explained via our current genetic inheritance evolutionary model as this kind of rapid adaptation simply could not have occurred by Darwinian means. Instead, it seems that these communities recovered and became ancestrally resistant to these same pathogens and our more recent molecular insights help explain just how this highly adaptive, rapid robust resilience works.

In summary, Nature appears to have an incredibly long-term memory for such pathogen/host battles of the past – leaving us with something of immense value to pass on silently to our children. Therefore,  even if we had all but forgotten these devastations – thankfully, our immune cells haven’t.

The history of successive onslaughts throughout the generations of some of the deadliest contagions known to humankind is inscribed in the charts presented throughout this study which mainly focuses on Ireland, with comparative data from several other nations, thus, these charts and graphs illustrate, in real time, our shared ancestral battle with the bugs. The overarching picture is that the identified pattern is of a near-simultaneous rise and dramatic decline in death rates from the same contagions for broadly the same timeframe –  is that it is an almost universal phenomenon and follows the natural principle of, what goes up, must also come down.

Thankfully, as this study aims to demonstrate, it would appear that we can now count our children because our ancestors have had the Plague, the Pox and just about everything else that has ever circulated in the past.  Now, isn’t that a relief?

Read on to explore natural immunity within its historical context and the newly emerging molecular science behind it...



How was the War on Bugs Won?

Fig. 1Fig. 4: Comparative scaled charts for all annual number of deaths recorded for all the major epidemic diseases in Ireland since first officially recorded. Charts generated using annual statistics reports since records began – “Annual Reports on Marriages, Births and Deaths in Ireland, from 1864 to 2000” courtesy of An Phríomh-Oifig Staidrimh, Central Statics Office CSO, link. © Copyright

It is difficult to grasp just how many deaths occurred in Ireland from infectious disease over the course of time. As you can see from the above charts in Figure 4 (showing the relative scale of mortality), some diseases were significantly deadlier than others. Compare, for instance, the annual death toll at its peak from TB to Smallpox which is discussed in greater detail in their relevant topics within this series. Figure 5 shows a range of once that these, irrespective of whether they are viral or bacterial become significantly less deadly, particularly by the mid-20th Century.

Note that some diseases such as Tetanus, Chickenpox, Mumps and Rubella are not illustrated above, as their impact on populations was so minuscule.

Fig. 5: Comparative charts showing the annual number of deaths recorded for many major epidemic diseases – bacterial and viral in Ireland since first officially recorded. Note the significant decline post mid-20th Century. Charts generated using annual statistics reports since records began – “Annual Reports on Marriages, Births and Deaths in Ireland, from 1864 to 2000” courtesy of An Phríomh-Oifig Staidrimh, Central Statics Office CSO, link. © Copyright

The essential pattern from the above charts is that all infectious diseases became significantly less deadly over time – to the point where they no longer register on the graphs above. This dramatic decline in deaths is not of course peculiar to Ireland, as irrespective of which disease we are talking about, or in which region we are viewing in the developing world for a similar timeframe, this great mountain of historical devastation dramatically declined – essentially, as discussed here, this is without our intervention.

Twentieth Century Mortality Trends in England and Wales

“Infectious diseases have declined to low levels, with the epidemics of the early part of the century no longer occurring”.

Griffiths and Brock, (2003) Office for National Statistics [1]

For comparative graphs to those from Ireland, see Thomas McKeown’s publication for England and Wales: The Role of Medicine: Dream, Mirage, or Nemesis? (1979) [2].  Again, these same type diseases are seen to become significantly less deadly across the board in the U.S. as well as seen in the study, ‘Annual summary of vital statistics: trends in the health of Americans during the 20th century’.

Annual summary of vital statistics: trends in the health of Americans during the 20th century

the beginning of the 20th century, the leading causes of child mortality were infectious diseases, including diarrheal diseases, diphtheria, measles, pneumonia and influenza, scarlet fever, tuberculosis, typhoid and paratyphoid fevers, and whooping cough. Between 1900 and 1998, the percentage of child deaths attributable to infectious diseases declined from 61.6% to 2%.

Guyer et al. (2000)  Paediatrics [3]

For comparative graphs of the dramatic decline of deaths throughout the earlier part of the 20th Century in the U.S.  See: Trends in Infectious Disease Mortality in the United States During the 20th Century (1999) by Armstrong et al, for graphs [4]. Also graphs of the decline of infectious diseases, again relating to the U.S. Infectious Diseases and Human Population History, (1996) by  Dobson and Carper [5].

Certainly, judging by the above graphs and historical records in general, by the earlier part of the 20th Century, our developing nations were becoming significantly safer for infants in particular that they were some decades before. This and a very similar decline in highly infectious diseases for essentially the same diseases are also noted as far north as Iceland corresponding to a comparable timeframe.

The Development of Infant Mortality in Iceland, 1800–1920

The great epidemic infant and child killers of the nineteenth century, such as measles and whooping cough, had lost much of their virulence. Occasionally, they were even successfully coped with in individual places with quarantine measures. By 1920 Iceland had become relatively safe for infants and young children in comparison with the dreadful situation prevailing around the mid-nineteenth century.

Loftur Guttormsson and Ólöf Garðarsdóttir (2002) [6]

What is perhaps more remarkable, is the fact that this common pattern of deaths from once deadlier diseases behaved similarly within nations on the other side of the world such as Australia as indicated in the two excerpts that follow:

Death registration and mortality trends in Australia 1856–1906

The age-standardised rate of all-cause mortality peaked at around 2,000 per 100,000 population in 1860—a year of fearsome epidemics. An important turning point occurred in 1885, after which mortality declined steadily and with less annual variation. The death rate fell from 1,600 in 1885 to under 1,000 in 1906, a fall of one-third over two decades.

Michael Willem de Looper (2014), Abstract, p. iv [7]

Epidemiologic Transition in Australia: The last hundred years

Long-term changes in major causes of death Australia experienced substantial changes in cause-specific mortality over the period 1907 to 2012 … mortality from infectious diseases decreased substantially during the first half of the twentieth century: in 1907, infectious diseases accounted for 16 per cent of the total standardised mortality rate for males and 23 per cent for females, but by 1946 accounted for less than 6 per cent for both sexes, and decreased to insignificant levels by 1960.

Booth,  Tickle and  Zhao (2016) [8]


Fig. 6: Dramatic decline in deaths from some of the greatest killer infectious diseases (mainly affecting children) in the pre-vaccine era.- Ireland (chart generated by A. Parent using annual statistics reports since records began – “Annual Reports on Marriages, Births and Deaths in Ireland, from 1864 to 2000” courtesy of An Phríomh-Oifig Staidrimh, Central Statics Office CSO, link. © Copyright Fig, 1a: U.S. comparable data. Source: Tavia Gordon, Public Health Reports, (1896-1970), Vol. 68, No. 4 (Apr. 1953), figure. 3.  Link to PDF The charts above compare the actual deaths recorded officially for Ireland since records began with deaths per 100, 000 from the United States. Below are comparable charts relating to the same dramatic decline in these same diseases as recorded from England and Wales for infants and children.

Take for example Figure 6, comparing a few of such major diseases where deaths from these diseases declined throughout the 20th Century in as far-flung nations as Ireland and the U.S. Deaths from the Measles virus or the bacterial pathogens known as: Pertussis (whooping cough) and Scarlet Fever – the other great killers of the 19th and earlier 20th Century – particularly amongst children, similarly plummeted according to a near identical pattern irrespective of the diversity or geographical location of our developing nations.

When we compare the decline in deaths from Scarlet Fever, Whooping Cough (Pertussis) and Measles seen within the above charts from such diverse regions as Ireland and the U.S. with graphs generated from England and Wales, we find once again, a very similar pattern of decline as seen in Figure 7. The only real difference between them all is that of number or rate of deaths annually which of course scales according to population sizes between these respective regions. For instance, if we removed the number individual deaths (as all the Irish charts employ), or the rate of deaths (used by most other more populous nations – per 100,000 or sometimes per million if their population is very large), apart from scale, these graphs would be difficult to tell apart.


Fig. 7: Adapted graphs based upon figures: 4.15 (Scarlet Fever), 4.24 (Whooping Cough/Pertussis) and 4.18 (Measles) showing rates of annual death rates per 100,000 of the population in England and Wales from 1901 – 2000. The shaded area represents post-WWII, after,Smallman-Raynor, M, Cliff, A (2012), Atlas of Epidemic Britain: A Twentieth Century Picture, Oxford University Press, Oxford. p.50, figure 4:18 (Measles); p. 52, figure 4:24 (Whooping Cough); p.49, figure 4:15 (Scarlet Fever).

Regarding the commentary about the above charts adapted for the purposes of this study (Fig. 7), the following statistics corresponds in percentage terms (not actual numbers of deaths as England and Wales would have a much larger overall population size compared to Ireland for the same period) very closely to what we observe in the Irish charts for the same diseases over the same timeframe.

Atlas of Epidemic Britain: A Twentieth Century Picture

A total of 67, 791 deaths from scarlet fever were recorded in England and Wales during the twentieth century, with the overwhelming majority (over 99 percent) occurring in the period 1901-45…
A total of 274,347 deaths from measles were recorded in England and Wales during the twentieth century, with over 98 percent occurring in the period 1901-45…
A total of 233,698 deaths from whooping cough were recorded in England and Wales during the twentieth century, with 97 percent occurring in the period 1901-45…

Smallman-Raynor, M, Cliff, A (2012), pp. 50, 52, 49, [9]

Causes of Death: A Study of a Century of Change in England & Wales

It is interesting that 3%, 2% and 4% of the reduction in mortality rate between 1901 and 1971 was due to whooping cough, measles and scarlet fever, respectively, but none of the decline in the mortality rate after this period. This is because by 1971 the mortality rate from these diseases already was extremely low.

Baillie et al.  (2012), p.6. [10]

This is just an example of the commonality of the decline in deaths over the same period and by similar percentages of certain diseases: Measles, Pertussis and Scarlet Fever across far-flung nations.

Not by our interventions?

In Thomas McKeown’s study dating to the late 1970s, The Role of Medicine: Dream, Mirage, or Nemesis? [11] he proposes, based upon the statistics of declining deaths within the context of our historical record of medical practice, that our medical intervention cannot, for the most part, be the direct cause of this decline – as these interventions came either too late or were not available at all to account for the almost universal decline in deaths from almost all of these once deadlier contagions of the past.

For instance, almost all of the previously more deadly diseases declined most significantly throughout the first half of the 20th Century, where there was a near 99 percent reduction in deaths in many regions as discussed above from the beginning of the 1900s if not earlier in some cases, to almost zero per by 1945 or the end of the Second World War (WWII), a time when antibiotics were only becoming more widely available which could begin combating the deadlier effects of many diseases and some antibiotics came later still depending upon specific infections.

Antibiotics are also only useful in fighting a disease that is bacterial and therefore, even taking into account their relatively late availability, cannot explain in any way for the decline in deaths from viral diseases that are discussed throughout this study. Nor can many of our vaccine or inoculation interventions be correlated directly with either the most significant decline in deaths, or the final demise of all the diseases discussed here as they either came too late – after the fact – or were not implemented at all.

This, of course, begs the question as to what is the cause of such an almost universal phenomenon in terms of the dramatic decline in deaths from some of the most deadly diseases? Scholars such as Thomas McKeown, suggest that other factors such as economics, improved living standards, better nutrition and a cleaner environments (the hygiene hypothesis as it is sometimes referred to) have commonly been offered as possible driving factors in the overall decline in infectious disease, as it now looks very like our medical interventions played a, perhaps surprisingly, small part in the historical and most major decline of deaths throughout the 20th Century – which is essentially the finding of this present study.

However, although this present study broadly supports McKeown’s conclusions regarding the fact that our medical interventions did not directly cause the decline in deaths from infectious diseases throughout the past few hundred years, the evidence that emerged from this present investigation does not support the alternative proposal offered by McKeown and others to account for the significant and often dramatic decline in deadly contagions throughout so many diverse nations for approximately the same timeframe. Their proposal simply doesn’t fit the data, or the historical record when we dig deeper into the context, rise and fall pattern over the course of time for each of the major diseases under discussion throughout this Natural Immunity Series.

This study will offer instead, a natural biological explanation as it relates to generational immunity over the course of time that can explain the almost universal pattern of decline in deaths from some of our most deadly contagions clearly evidenced throughout our nations as they developed into the modern era.

These more recent insights into the dynamic and sophisticated interplay between pathogens and us as their hosts are well supported by the historical record and matches the overall pattern of death statistics in general than either the medical intervention or the hygiene/population dynamics offered by others as an alternative. This present study revisited historical accounts of each of these plagues of humanity in the light of the findings produced from several lines of molecular investigations and found that this matched the data much better than other proposals offered thus far.


References for Intro & Part One

1. Griffiths C and Brock A (2003) Twentieth Century Mortality Trends in England and Wales. Health Statistics Quarterly, Issue 18, pp. 5–17. [Available online as PDF]–18–summer-2003/twentieth-century-mortality-trends-in-england-and-wales.pdf
2 Mc Keown, T (1979) The Role of Medicine: Dream, Mirage, or Nemesis? Basil Blackwell, Oxford [Available online as PDF]
3 Guyer B, Freedman MA, Strobino DM, Sondik EJ. (2000) Annual summary of vital statistics: trends in the health of Americans during the 20th century, Pediatrics. Vol. 106, [6]: pp. 1307-17.
4. Gregory L. Armstrong, G.L, Conn L.A, Pinner, RW (1999) Trends in Infectious Disease Mortality in the United States During the 20th Century, JAMA. Vol. 281 [1]: pp.61-66. DOI: 10.1001/jama.281.1.61
5. Dobson, AP. and Carper, ER (1996) Infectious Diseases and Human Population History: Throughout history the establishment of disease has been a side effect of the growth of civilization, BioScience, 46, Issue [2,] pp. 115–126, DOI: 10.2307/1312814 [Available online as PDF]
6 Guttormsson, L and Garðarsdóttir, Ó (2002) The Development of Infant Mortality in Iceland, 1800–1920, Hygiea Internationalis, An Interdisciplinary Journal for the History of Public Health, Vol. 3 [1] pp. 151 – 176, PDF · [Available online as PDF] DOI: 10.3384/hygiea.1403-8668.0231151
7 De Looper, MW (2014) Death registration and mortality trends in Australia 1856–1906, Abstract, p. iv. PhD Thesis: The Australian National University [Available online as PDF]…/De%20Looper%20Thesis%202015.pdf
8 Booth, H, Tickle, L, Zhao, J (2016) Epidemiologic Transition in Australia: The last hundred years, Canadian Studies in Population Vol. 43, [1–2]: pp. 23–47.
9 Smallman-Raynor, M, Cliff, A (2012), Atlas of Epidemic Britain: A Twentieth Century Picture, Oxford University Press, Oxford. p.50, figure 4:18 (Measles); p. 52, figure 4:24 (Whooping Cough); p.49, figure 4:15 (Scarlet Fever).
10 Baillie, L. and Hawe, E. (2012) Causes of Death: A Study of a Century of Change in England & Wales, OHE (Office of Health & Economics) p.6.
11 Mc Keown, T (1979) The Role of Medicine: Dream, Mirage, or Nemesis? Basil Blackwell, Oxford [Available online as PDF]

 Continue reading rest of series as it is published:

Part Two:
Whatever happened the Bubonic Plague and what has Chickenpox got to
do with it
Part Three:
The Many ‘Typhoid Marys’
Part Four:
Typhus: Filling in the Gaps
Part Five:
Cholera: The Disease that Inspired Bram Stoker to Write Dracula? And A Tale of Two Pathogens
Part Six:
Scarlet Fever Returns: but it is a lot less deadly
 Part Seven:
Don’t Count Your Children Before They Get The Pox
Part Eight:
Would we survive Smallpox if it escaped from a Lab today?
From the Plague to the Pox

Next episode: Part Six: Scarlet Fever Returns But it is a Lot Less Deadly

Use the contact form below for updates of forthcoming series and book (Beta readers required – going to publication Autumn 2018…) or simply get in touch via


Part Two (of ‘Don’t Count Your Children Until they’ve had the Pox’) WHATEVER HAPPENED TO THE BUBONIC PLAGUE & WHAT HAS CHICKENPOX GOT TO DO WITH IT?

Click Here for last week’s article: Part One & Intro

Part Two of Weekly Series:





They’ve had


P O X!




M.B. O’Hare



Contact DiG-Press via email for more information:

© M. B. O’ Hare. 2018.

May be used for educational purposes without written permission but with a citation and copyright notice linked to this source.


Can We Now Count Our Children?
 Part One:
How was the War on Bugs Won?
Part Two:
Whatever happened the Bubonic Plague and what has Chickenpox got to
do with it
Part Three:
The Many ‘Typhoid Marys’
Part Four:
Typhus: Filling in the Gaps
Part Five:
Cholera: The Disease that Inspired Bram Stoker to Write Dracula?
Part Six:
Scarlet Fever Returns: but it is a lot less deadly
 Part Seven:
Don’t Count Your Children Before They Get The Pox
Part Eight:
Would we survive Smallpox if it escaped from a Lab today?
From the Plague to the Pox

 Part Two

Whatever happened the Bubonic Plague and what has Chickenpox got to do with it?

BBC History

‘there were hardly enough living to care for the sick and bury the dead’
…scarcely a tenth of mankind was left alive.
James, 2011, ‘Black Death: The lasting impact’  

A plague tsunami swept across Europe in the year 1348 wiping out more than a third of its population. By the late summer, the Black Death descended upon Irish shores with a particularly harsh impact in the urban centres which took its greatest toll in the dead of winter. Spreading out in a second wave reaching its tentacles beyond to the most desolate hills in search of fresh victims, this plague knew no social boundaries as Nobles, Clergy, Merchants and Peasants either survived the disease – gaining immunity, or succumbed and died.

‘1348: A Medieval Apocalypse – The Black Death in Ireland’

1348 was one of the darkest years in European history. The most deadly of all diseases – the Black Death – swept across the continent reaching Ireland in the late summer. Within twelve months over one-third of the population had died. Towns and villages were abandoned.
Dwyer, 2016. Book Synopsis 

…But, Rats and their fleas may not be guilty after all…

rat heap

Fig. 1: The Grime Reaper Rat on a pile of rat corpses. Illustration of what archaeologists should have found, but didn’t – thus indicating that rats and their fleas may be innocent in being the true cause of the rapid and widespread devastation of the Plague during the middle ages.

Now looking at the archaeological evidence, as it turns out, there is a serious lack of evidence for great heaps of dead black rats.

‘Black Death? Rats and fleas finally in the clear’

…Archaeologists and forensic scientists … have examined 25 skeletons … Analysis of the bodies and of wills registered in London at the time has cast serious doubt on “facts” that every school child has learned for decades: that the epidemic was caused by a highly contagious strain spread by the fleas on rats…
Mortality continued to rise throughout the bitterly cold winter, when fleas could not have survived, and there is no evidence of enough rats… In sites beside the Thames, where most of the city’s rubbish was dumped and rats should have swarmed, and where the sodden ground preserves organic remains excellently, few black rats have been found.
Thorpe, 2014, 

As noted above, we also know that the plague was spectacularly lethal during the winter months and the fleas that are supposed to be the culprits in spreading it via black rats, would not have been able to survive in this late season. Similarly, this was also the case in Ireland judging by the historical records.

‘Unheard of mortality’ The Black Death in Ireland

The plague raged in Dublin between August and December, setting a pattern for the terror it would spread through other parts of the country…
Thorpe 2014, ‘Black Death? Rats and fleas finally in the clear’

So if no amount of cleaning up rat infestations could have curtailed the spread – as the rats and their fleas now appear to be off the hook, what caused such a devastatingly rapid and severe spread of this great pestilence?

A clue might lie in the following. If anyone is old enough to remember actually singing this little rhyme below, having no idea whatsoever what we were singing about, then you might be interested to know what it was all about.

Ring a’ ring a rosies,

A pocket full of posies,

A Tishoo,a tishoo,

We all fall down.


Bugl, 2008, 8, ‘History of Epidemics and Plagues’ 

Apparently, according to Bugl in the History of Epidemics and Plagues’, the common interpretation of the Rosies refers to rosary beads (the religious item used for prayer – presumably in the hope that this would provide protection from the plague and imminent death) and the part of the rhyme when the children hold hands, forming a circle, presumably indicates the ring.

It seems that the pocket full of posies suggests wildflowers to mask the odour of plague victims. However, further research on the medical interventions of the era would indicate that flowers and herbs (posies) may have been used as protection as well. But, perhaps the most interesting part of the rhyme which gives us the big clue, is that last line (the fun part for children if you didn’t know any better, as they all collapse unto the ground in a giggle at the end), relates to a mock sneezing “A Tishoo, A Tishoo,” – which strongly points to the pneumonic (lung) form of transmitting the plague rather than the bubonic means of transmission, as they all fall down after being sneezed on.

As the article excerpt below indicates, the pneumonic and bubonic plague are essentially the same disease; and are simply manifested in different ways within the body.

Risk of Person-to-Person Transmission of Pneumonic Plague

Bubonic plague never spreads directly from one person to another. The bacteria may reach the lungs of people through hematogenous spread… Pneumonic plague is the only form of plague that can be transmitted from human to human.
Kool and Weinstein, 2005

Therefore, the sneezing form (pneumonic) can originate from the bubonic plague by making its way into the lungs via the bloodstream (hematogenous – meaning to spread by the blood) (see below),, as suggested above. This lends greater support to the means by which the Plague could have spread with such initial devastation – now having a way to directly pass from person-to-person. In other words, we do not necessarily require rats and their fleas to explain the wildfire type spread of this disease, at least during the Middle Ages.



1. Producing blood.

2. Originating in or spread by the blood.


Stedman’s Medical Dictionary (2002)

We can now begin to imagine how the Plague could have possibly arisen  and gotten a foothold – at least initially via infected rats in its bubonic form (hence the term Black Death in some cases), and if it had found a way of entering the bloodstream which, we now know is medically possible and common enough judging by modern studies, we can see just how more easily spreadable the pneumonic form (via sneezing etc) would be compared to the rat/flea-borne bubonic plague form – which would have been more easily spotted than the sneezing form.

We could, therefore, suggest that the flea-infested rats may have been the spark, but the uninitiated population (new virgin hosts for the pathogen) provided the kindling and it all went up like a tinderbox as the growing European shipping commerce fanned the flames of the burgeoning metropolitan centres during the Middle Ages.

However, the good news is that, just as rapidly as this devastation spread, it also appears to have burnt itself out almost as swiftly. Seemingly, it had consumed just about all that it could find in its path and those that remained standing would have become immune because of it.

The Black Death in Ireland


Today we have the benefit of hindsight. We know, as fourteenth-century people suspected, that the mortality caused by the bubonic plague of the Black Death was the worst demographic disaster in the history of the world. We also know that the mortality came to an end in the first outbreak soon after 1350; contemporaries could not have known this would happen – so far as they were concerned everyone might well die…
Kelly, 2001, ‘Unheard-of Mortality’ 

As the plague was virtually unheard of after the 1350s in Ireland and most other parts of Europe, one might wonder where it went and would we survive the Plague if it rekindled itself? As it turns out, it did come back within historical living memory as documented for Ireland as we prepared for its reemergence as described below:

1900: Ireland’s last bubonic plague scare

While bubonic plague evokes images of the Middle Ages, Ireland has had more than one brush with the dreaded disease. As recently as the year 1900, ports across Ireland prepared for an imminent outbreak of the Black Death…
…The last great plague scare in Ireland began after the illness broke out in Glasgow in August 1900. Ireland with its constant and frequent traffic with the Scottish port was immediately at risk of infection… As the death toll in Glasgow reached 13 by September 8th 1900, petty politics in Ireland hamstrung preparations to prevent an outbreak… Nevertheless in spite of such attitudes all vessels arriving in Ireland from Glasgow continued to be subjected to rigorous checks. Meanwhile the Glaswegian authorities, not only isolated those who contracted the disease but also those who lived in close proximity to them. This drastically reduced contagion and by the end of September there was a dwindling number of new cases.
Dwyer  2016, ‘1900: Ireland’s last bubonic plague scare’

Fortunately, the new cases began to quickly fade as indicated above, and perhaps it was to do with the containment measures, but more recent outbreaks would suggest otherwise. For instance, modern-day incidences and more recent historical experiences with outbreaks are rather puzzling as the Plague itself, even in its pneumonic form doesn’t appear to have the great impact that it once had. I.e., even if it does escape out into the unsuspecting public, which it has done on a number of occasions in more recent times, it has thankfully turned out to be surprisingly tame.

Plague has received much attention because it may be used as a weapon by terrorists. Intentionally released aerosols of Yersinia pestis would cause pneumonic plague. In order to prepare for such an event, it is important, particularly for medical personnel and first responders, to form a realistic idea of the risk of person-to-person spread of infection…
The disease resulting from direct infection of the airways is usually called primary pneumonic plague. This form would also occur after an intentional release of aerosolized Yersinia pestis…
Since 1925, person-to-person transmission of pneumonic plague has not been documented in the United States. From 1925 to 2003, there were 447 cases of plague reported to the CDC, and 48 developed into secondary pneumonic plague. Thirteen cases of primary pneumonic plague were reported in the same period; 5 of these were caused by cats with plague pneumonia, 1 was associated with caring for a sick dog, and 3 cases were laboratory-acquired.
In 4 cases, the origin of the infection remained unknown (CDC; unpublished data) … None of the contacts of these 61 patients with pneumonic plague seem to have developed the disease.
Kool and Weinstein,  2005  

One of these cases is worth reviewing in order to demonstrate just how tame the plague appears to have become compared to when it was circulating in the Middle Ages. For instance, although its only victim did unfortunately die, it was discovered after the fact that she had the real pneumonic Plague form – (they thought she had actual pneumonia at first as Plague is so rare these days) and it was sometime later when she had already exposed quite a number of people, including small infants in the day-care centre where she worked, that the penny finally dropped when the medical people realised what had just happened. This is described in the excerpted article below:

Discover Magazine

‘Will the Black Death Return?’

On October 2, 1980, a 47-year-old woman from south lake Tahoe, California, lost her 9-month-old pet cat to an acute infection. Three days later, the woman’s own temperature shot up, but she still went to her job at a day-care center. The fever worsened; she developed chest pains and shortness of breath. Two days later she drove herself to the hospital. The diagnosis was pneumonia, and she was treated with tetracycline. Shortly afterward the woman died.
Not until four days later did anyone realize that the woman had died of plague…
….Fearing that treatment might arrive too late, doctors rushed prophylactic antibiotics to the children and staff at the day-care center.. Luckily, no one exposed to the woman fell ill.
Orent, 2001

Under the same conditions of the Middle Ages, those around the infected and caring for the sick died in large numbers and the Plague spread rapidly to hundreds more, leading to thousands and ultimately millions, yet, in our more recent era, it is thankfully a completely different story.

Of course, this then raises the question: well, the plague must have changed somehow, as we know those clever bacteria can adapt very rapidly, unlike our relatively fixed genetic code. Perhaps this wasn’t the once deadly plague? Maybe it had become tamer over the centuries? This very question has recently been answered by extracting DNA from the original once deadly Plague:

Black Death? Rats and fleas finally in the clear’ Discovery Magazine

By extracting the DNA of the disease bacterium, Yersinia pestis,.. [T]o their surprise, the 14th-century strain, the cause of the most lethal catastrophe in recorded history, was no more virulent than today’s disease. The DNA codes were an almost perfect match…
Thorpe, 2014

Just think about that for a moment. This is the same once lethal plague that once killed millions some few hundred years previously and now, even if some mad terrorists release it into the public, we might not even notice that it is the pneumonic form of the Plague at all as no one would have black bubonic type lumps to say otherwise. Of course, this is really good news for most of us – I am sure we wouldn’t all escape, but we simply shouldn’t worry too much about such an event in our day and age.

However, it still doesn’t explain how we became so resistant to such previously deadly contagions like the Plague in the first place, and especially, because it hasn’t changed (genetically speaking) one jot since its devastation of the Middle Ages. A clue lies in the following excerpt.

Scientific America

How Black Death Kept Its Genes but Lost Its Killing Power

The newly sequenced genome of the plague-causing bacterium Yersinia pestis suggests human adaptations are what have kept this disease in check… The global population has likely built up some immunity from centuries of exposure to the pathogen.
Harmon, 2011 ‘How Black Death Kept Its Genes but Lost Its Killing Power’ [Video], 

Seemingly we have become immune over the centuries and the mechanism may lie in a very unlikely source: another friendlier pathogen in the form of some familiar viral characters that most of us have had some experience with over the generations. This is where Chickenpox and its relatives come into the saga of explaining whatever happened to the Plague per se.

For instance, recent molecular studies have revealed something rather surprising about the fate of the once much more lethal Plague. In essence, scientists are now finding that if mice can combat the deadly form of the PLAGUE with common viruses most of us are already infected with, it is quite possible and highly likely, that we do the same.

The Good Thing About Herpes

     The herpes family of viruses can have a surprising upside–it can protect against the bubonic plague and other bacterial contagions, at least in mice. …Nearly all humans become infected with multiple herpes virus family members during childhood. These germs not only include the herpes simplex viruses, which lead to cold sores and possibly genital herpes, but also the diseases responsible for chickenpox and “mono,” as well as several less well-known ailments. Herpes infections have bedeviled animals for more than 100 million years…
…The scientists discovered latent infections with these viruses could protect mice from bacterial infections, including Yersinia pestis, which causes bubonic plague… findings detailed in the May 17 issue of the journal Nature. The herpes viruses spur the immune system to boost levels of a protein hormone called interferon gamma “that in effect puts some immune system soldiers on yellow alert, causing them to patrol for invaders with their eyes wide open and defense weapons ready,” Virgin said. As a result, the bacteria grew more slowly and were less likely to kill the mice.
Choi, 2007

The Herpes family of viruses are, as noted above, very common and most of us already have these living inside us. Essentially, it looks like the host (that’s us) learns to defend itself making it impossible for critters to continue their destruction and it does this by slowing down the virus’ s ability to replicate in the highjacked cells and stave off the worst effects of the bacterial Plague, giving our own immune systems time to respond. The more the immune system does this: the more efficient it becomes and it does this, apparently, via the boosting of our immunity through simple exposure to things such as Chickenpox.

Basically, the Plague bacteria have to adapt or suffer the consequences of our mighty defence. They usually learn to behave themselves and become less invasive and quite tame. This immunity comes essentially from allowing the typically benign childhood disease of Chickenpox, for example, to circulate naturally so that all ages keep boosting their immune systems as you will see in the article below.

As Chickenpox is part of this family that seems to be implemented in the reason why we no longer are dying in our millions from the plague, it may be important to keep it around as it now appears that it is quite important to let it circulate naturally for the reasons outlined below. The article relates to the fact that the UK is considering introducing a vaccine into the childhood schedule to tackle Chickenpox and looking to the experience in the U.S. where the vaccine has been included in the infant and childhood schedule for some time now. The situation in Ireland is somewhat similar to that of the UK as we have never had a routine vaccine given for Chickenpox.

Chickenpox, chickenpox vaccination, and shingles

Chickenpox in the United Kingdom, where vaccination is not undertaken, has had a stable epidemiology for decades and is a routine childhood illness. Because of vaccination, chickenpox is now a rarity in the USA. In the UK vaccination is not done because introduction of a routine childhood vaccination might drive up the age at which those who are non‐immune get the illness (chickenpox tends to be more severe the older you are), and the incidence of shingles may increase. The United Kingdom is waiting to see what happens in countries where vaccination is routine.
…We know that exposure to chickenpox can significantly prevent or delay shingles (by … boosting of immunity)… Increased annual chickenpox rates in children under 5 are associated with reduced shingles in the 15–44 age group. Having a child in the household reduced the risk of shingles for about 20 years, the more contact with children the better, and general practitioners and paediatricians have a statistically significant lowering of risk,.. possibly because of their contact with sick children (teachers did not have a significantly reduced rate)…
If there is less chickenpox in children then there will be no boosting of immunity by exposure to chickenpox for middle and older aged people and thus there will be more shingles, at least until all the elderly have been vaccinated as children but this assumes that immunity conferred by vaccination is lifelong… The greater the chickenpox vaccination rates the higher the initial incidence of shingles would be until everyone was vaccinated (in other words until those of us my age who harbour varicella zoster virus in our nervous ganglia die off). It may be that a less than 100% cover by vaccination might reduce the combined chickenpox and shingles morbidity by allowing the virus to circulate in the population with only minor increases in the age of chickenpox while boosting immunity to shingles…
The extent of decline in vaccination induced immunity to chickenpox over future years is not, of course, known and neither is the proportion of those vaccinated in the USA from 1995 that will become susceptible to “geriatric chickenpox.”
Welsby, 2006, 351-52 


Remember that, based upon the above evidence, all in all, it now appears that no amount of capturing rats and cleaning up flea infestations would have helped reduce the death toll of the disease even in our modern era, as the evidence now strongly supports the black rat’s innocence – along with their flea companions – in being the harbingers of death and destruction during the Middle Ages.

Furthermore, our medical interventions cannot account for the rapid decline of deaths in such a short space of time in most regions as we never had a vaccine to try to eradicate the disease or antibiotics back then. And I don’t think the plague doctors going around with prodding sticks and bird mask with beak filled with herbs and poisons did anything other than protecting them against getting the disease itself – if it protected them at all – we don’t know. Seemingly, the plague resolved itself naturally as there are still cases in parts of the U.S. annually that typically don’t end in death and their contacts are not falling down in their millions after going: “A Tishoo…A Tishoo…” thinking it was a bad cold or the flu that turned to a case of pneumonia.

It looks like Nature has tamed this once much more deadly beast which – although it is the same disease as that of the Middle Ages (genetically speaking) that once killed millions, in more modern times via our exposure to natural viral infections with the Herpes Family over many generations  our defences against the Plague have gotten fairly robust. This seems a reasonable trade-off as it beats having the Plague compared to providing a home for something as benign (for the most part) as cold sores (just don’t go kissing any new-born infants), or childhood Chickenpox.

Perhaps, therefore, we are very fortunate here in Ireland and indeed, the UK and the other regions in Europe where they do not currently have the Chickenpox vaccine along with several boosters in the childhood schedule, as most children still  get the disease naturally, gaining life-long immunity (which is incredibly long compared to the much more variable and significantly shorter immunity we now know that all vaccines studied can offer).

Exposure to the real Herpes Family disease seems a much more beneficial option all round, as having something like Chickenpox, not only seemingly boosts natural resistance to the potential latent virus eruption later in life in the form of fairly painful Shingles but, by allowing the disease to circulate naturally, we also expose children at the appropriate age – thus reducing complications and confer life-long immunity against ever having Chickenpox again. Perhaps, of greatest importance, we may be most fortunate in allowing the Herpes Family of viruses, (of which Chickenpox is one member) to circulate naturally as it seems to be doing a fairly good job at keeping the more lethal impact of the Plague at bay.

So, if the Plague does escape from the lab again, as it has done on a number of cases in the past, try to find some children having a pox party and see if they’ll let you in.

Next week: Part Three: The Many ‘Typhoid Marys’.

Fill in the contact form below for updates on the Ten Part weekly series: Don’t Count your Children Before they’ve had the Pox.

References to Part Two

[1] James, T. (2011) Black Death: The lasting impact, BBC, (17th Feb, 2011).[Available online at]

[2] Dwyer, F (2016) 1900: Ireland’s last bubonic plague scare (5th Jan, 2016), Irish History Podcast [Available online from]

[3] Thorpe, V. (2014) Black Death? Rats and fleas finally in the clear, (30th March 2014). [Available online at],

[4] Thorpe, V. (2014) Black Death? Rats and fleas finally in the clear, (30th March 2014). [Available online at],

[5] Bugl, P (2008) History of Epidemics and Plagues’ p.8. [Available online at as PDF]]

[6] Kool, J.L., and Robert A. Weinstein R.A (2005) Risk of Person-to-Person Transmission of Pneumonic Plague, Clinical Infectious Diseases, Vol.40, Issue 8, (15 April 2005), Pp. 1166–1172, [Available online ]

[7] Stedman’s Medical Dictionary (2002) Definition of ‘hematogenous’,  American Heritage, Houghton Mifflin Company, U.S.A. [Available online at Link]

[8] Kelly, M. (2001) Unheard-of Mortality….The Black Death in Ireland, History Ireland: Issue 4 (Winter 2001), Medieval History (pre-1500), Vol. 9, [Available onlin at]

[9] James, T. (2011) Black Death: The lasting impact, BBC, (17th Feb, 2011) [Available online at]

[10] Findwyer (2016) 1900: Ireland’s last bubonic plague scare (5th Jan, 2016), Irish History Podcast [Available online from]

[11] Orent, W. (2001), Will the Black Death Return?, Discover Magazine, (1st Nov, 2001), [Available online at]

[12] Thorpe, V. (2014) Black Death? Rats and fleas finally in the clear, (30th March 2014). [Available online at],

[13] Harmon, K (2011), How Black Death Kept Its Genes but Lost Its Killing Power, Scientific America, (12th Oct. 2011), [Available online at Video]

[14] Choi, C.Q. (2007) The Good Thing About Herpes, Live Science (16th May 2007), [Available online from livescience]

[15] Welsby, P. D. (2006). Chickenpox, chickenpox vaccination, and shingles. Postgraduate Medical Journal, Vol. 82, [967], pp. 351–352. [Available online].







Everything is Scale-Dependent: “Something Universal is Going on…”(G. West – physics applied to biology)


”Everything around us is scale dependent…

It’s woven into the fabric of the universe…

It is truly amazing because life is easily the most complex of complex systems,…

‘But in spite of this, it has this absurdly simple scaling law. Something universal is going on …”

Johnson (1999, ‘New York Times’ 12th January, excerpts taken from an interview with G. West – physicist working on biological systems)


Whether it be: the growth rate of any organism from a gnat to an iguana, and from algae to great oak forests: everything seems to be governed by universal laws of fractal-like nested scales of complexity. The  Sigmoidal growth & development ‘S’ Curve is one of those laws that Nature appears to abide by. See info graphic above for the Sigmoidal Growth Curve.

Growth models based on first principles or phenomenology?

…growth curves are almost universally sigmoidal…

West et al (2004, Introduction)


As Physics begins to reunite with biology…for instance, as a result of his research, Geoffrey West (Physicist who collaborates with biologists) has come to the realisation that Nature is full of universal patterning that is predictable. As these identifiable scales of magnitude and fractal-like patterning are measurable, this is therefore a very powerful scientific tool which, can begin to reveal the previously unknowable aspect of growth and development: EVOLUTIONARY Species development.


There is something, an essential and indispensable something, which is common to them all, something which is the subject of all our transformations, and remains invariant (as the mathematicians say) under them all.

D’Arcy Thompson (1945, 1085)


The identification of the universal patterning embedded at every scale is not such a new concept. Indeed, there is a growing body of support for D’Arcy Thompson’s profound observations (see above quote) of the underlying nature of Nature. I have attempted to apply these universal scaling concepts (invariants) in an effort to discover a form of development we cannot so readily observe in real-time: the rate and patterning of evolutionary development of the species on every scale.

The initial investigation started with D’Arcy Wentworth Thompson’s (1860 – 1948) alternative evolutionary scenario (non-Darwinian) which could be best summarised as: SCALING LAWS EMBEDDED IN ALL LIFE & APPLIED TO THE DEVELOPMENT OF LIFE itself.

All in all, I believe that the above info graphic is the best summary that I can think to make regarding the essential essence of the discoveries made whilst researching the deep historical record of alternative evolutionary theories; naturalistic theories (and very much testable and empirically supported ideas of the past) which, I have come to believe, from simply following the evidence: has the potential to completely topple the entire Darwinian tree (roots and all).

The Search for the Laws of Self-Organization and Complexity

…A few deep and beautiful laws may govern the emergence of life and the population of the biosphere…

Kauffman (1996, 23)


If you are interested in finding out more about the Matryoshka (nested scaling laws) and how this model applies directly to evolutionary complexity, it is detailed with clickable links to all the scientific literature in Chapter One of a newly published e-book. It is available for Free as I believe that the information is so important that it should be shared widely and with as much ease as possible. So all I ask, if you go for the free copy, is to SHARE WIDELY so that others can find this information and access it for themselves.

evolution by other means book one cover resized for smashwords.pngTHIS IS THE FREE KINDLE E-BOOK VERSION

Click on Cover above for your free Kindle copy (you don’t need a Kindle to read it – you can just download the free app for your mobile device/computer etc from Amazon’s online store).

When you click on the link, you will find out more information about the book and its contents and you also have the option to pay something for the book by simply putting in an amount – it has a secure paypal transation attached, but you don’t have to use paypal if you don’t want. Otherwise, just download it for free: $0.00 and you will have your own copy delivered straight to your mailbox and/or to read there and then.

For Other Version: E-Pub etc click here

Click here for Kindle version on Amazon

You can go on to Amazon where you usually shop and simply do a search for “evolution by other means..?” I could not sell it on Amazon for Free, so it is a cheap as I could possibly make it (99c excluding VAT).




This is a preview of Chapter Three from forthcoming book on Evolution by Other Means…?

DNA nebula molecule compared


Alexander Graham Cairns-Smith

(Born 1931)



Cairns-Smith is a Scottish molecular biologist and organic chemist and his crystalline origins theory leads on naturally from the previous chapters, as it corresponds to the fundamental and inherent properties of patterns of scale, self-organisation, replication: ‘remembered’ patterning and modification according to environmental factors, that can be essentially, scaled up to possibly account for the evolution of the cells and the complex molecules of life – its code.

Smith-Cairns’ concept is not an alternative to the Darwinian model, as are many of the others presented in this book, but rather, it deals with the origins aspect of cellular life along with the code of life, that our current model has never fully addressed. Below is a short excerpt that should give an insight into his main hypothesis.

Life’s Crystal Code

To Alexander Graham Cairns-Smith, that glimmer may owe something to the sparkle of a crystal.

Cairns-Smith, an organic chemist at the University of Glasgow, sees a significant relationship between the structure of DNA molecules and the structure of certain kinds of mineral crystals. He says that while patterned structures that replicate themselves are common in the inorganic world of crystals, it is a rare quality in the organic world — DNA and RNA are the only organic molecules we know of that strongly exhibit this characteristic.?

Mullen (2009, ‘Astrobiology Magazine’ 19th March)


Essentially, Cairns-Smith’s novel proposal can be seen from the 1960s onwards via his many books and numerous articles on the topic of the self-replication of clay crystals in solution as a precursor to molecular life and its ability to replicate itself. Some of the main publications are listed as follows: The life puzzle: on crystals and organisms and on the possibility of a crystal as an ancestor, 1971, by A.G., Cairns-Smith, Toronto University Press [55]; Genetic takeover – and the mineral origins of life, 1982, by A.G.,  Cairns-Smith, Cambridge University Press [56]; Clay minerals and the origin of life, 1986, by A. G. Cairns-Smith and Hartman, H., (eds.,), Cambridge University Press. UK [57] and, Seven Clues to the Origin of Life – a scientific detective story, 1990, by A.G. Cairns-Smith, Cambridge University Press [58].

Essentially, Cairns-Smith’s concept, as it specifically applies to the clay crystalline matrix origin of coding complexity, not only proposes a useful model to account for rather humble beginnings of life from non-life, but he takes this one step further and suggests we may be looking at an actual ancestor when we observe the complex growth processes of such crystalline forms as stated in: Origin of Life, (ed.,) C. H. Waddington, Transaction Publishers, 2009 in the chapter entitled:

An approach to a blueprint for a primitive organism

We might think of the replication of the unit cell of a crystal, or better the replication of a pattern of dislocations, during the growth of a crystal…Rather than consider theoretical models of replication processes that closely mirror those of modern organisms we should perhaps look very hard at the simple processes of replication which already exist in profusion in the physico-chemical world, and to consider these not simply as models, but as potential ancestors.

Cairns-Smith (2009, 58)


Now, I would propose an ancestrally shared condition or system, rather than a literal ancestor, as discussed previously where evolution appears to be a process of simpler and more primitive systems that tend towards complexity and organisation on every possible scale, but Cairn-Smith’s model is certainly more than a simple model, and does, indeed appear to have a very real and tangible link to organic life as you will see further on in this chapter.

 Peeling back the Crystal-Coded Onion

… Life’s First Barcode?

…, clay mineral layers not only attracted certain chemicals from the environment to their surfaces, the mineral layers also acted as the first genetic information carriers, much as the base pairs in DNA do today.

“The objects that I’m particularly interested in are mixed-layered crystals, in which the crystal structure consists of beautifully formed layers packed on top of each other, but with an arbitrary sequence,” says Cairns-Smith. “In that respect, they’re like a DNA molecule, which has base pairs, little platelets inside it which are stacked on top of each other. It is the sequence of this stacking which creates the information.”

Cairns-Smith doesn’t think the clay mineral crystals were “alive” anymore than a DNA sample is thought to be alive. Instead, by acting as the first genetic materials for early life, clay mineral crystals created a link between the worlds of inorganic and organic chemistry.

At some point, life launched free of its inorganic genetic origins — the organic substances that evolved from chemical interactions on the mineral layers became stable enough to live apart from their birthplace, and complex enough to replicate themselves into the future.

Some mineral layer combinations probably worked better than others when it came to marshalling the organic molecules that were to eventually become genetic materials.

Mullen (2009, ‘Astrobiology Magazine’ 19th March)


Basically, I have outlined the main characteristics of crystal growth below, and emphasised, what I think are the most interesting facts regarding crystals as they correspond to Smith-Cairn’s hypothesis. This should help to get a broad feel for his concept. For instance, for anyone that doesn’t already know the fascinating properties of crystal growth (but I’m sure you do), this is just a brief overview reminder.  I will start with the snow-crystal or snow flake structures as they, like biological life, need a starter seed, a trigger to trigger growth (some inorganic material, just as a snowflake has to be first seeded from a speck of dust in the clouds). Then their growth pattern follows a very clear and predictable molecular (molecule bonding etc) pathway via hydrogen bonds in the case of snow-crystals.

A snowflake starts out as a basic geometric prism (always six-sided in the case of snowflakes or cubes as in salt crystals) and this informs the underlying pattern in every direction along the main axes in proportion to itself. Each level of growth is a complete scale of growth and this pattern will be repeated over and over again on all the finer scales until the crystal has reached the full capacity of its sustainable system. And all of this is in direct relation to its environment, temperature and surface conditions, water molecules and float rate etc.

Then of course they melt and the whole process can start over, if the conditions are right. Their final shape and form (even though they all follow the same fundamental principles of growth) there are modifications made according to the fluctuations in the growing conditions and hence: the expression no two snowflakes look the same comes to mind.

However, the type of crystal growth and form that Cairns-Smith uses such as rock crystals in a clay solution as outlined in the quote above, does highlight the rather amazing properties of memorised and replicated patterning, where, if a small part of the whole crystalline structure becomes dislodged as it forms; the parent matrix/lattice from which it came directs the growth and development matrix pattern of the daughter crystalline structure, this will vary slightly if its growing conditions/surface is different or changed in some way – modified.

Recall the concept emerging within the nested scales of complexity model, where a small change at the beginning can ultimately have quite a large effect further down the line, well, clay-crystal growth in solution is fundamentally similar and ultimately, conditioned in its overall shape and form by rules that are seemingly applicable and universal to almost all living structures as far as we can tell; just as much as to crystalline ones as well.

I should also point out that Nature does not grow one snow-crystal arm at a time, any more than a snow drop puts on one petal at a time. Each stage of fractal-like growth is a whole phase or stage and completes this stage before taking the self-similar repeating pattern to another more elaborate and complex (and typically larger) scale. In combination then, crystal growth gives us all the essential processes and principles embedded within life itself.

Crystal growth for instance, has the properties of fractal-like growth at different complete scales, patterned memory and its modifications according to environmental factors during growth that can be ‘remembered’, via imprinting that can be replicated ‘inherited’ allowing further divergent growth and has fundamental properties of predictable, measurable, fractal-like (self-similar patterns repeated at all scales) shape and form.

In other words, crystal growth also mirrors at its most fundamental level, all the main characteristics embedded within the genetic code, epigenetic modification processes, cellular memory and adaptation according to environmental conditions discussed in the previous chapters, only on a much more primitive scale of complexity.

Once again, it seems that we may be looking at building upon the same principles of earlier systems to evolve much more complex systems: nested scales of complexity. Therefore, in order to explore this concept fully, particularly with regard to the genetic code itself, we need to rewind the possible evolutionary scenario for the evolution of the gene code within the context of the cells and as complex organisms are made up of lots of interacting cells – this should begin to reveal the nested scales of complexity embedded within the evolutionary development process which is clearly in evidence from the very small and primitive to the very complex and large.

We will therefore start with a brief overview of what we can establish as the essence of how the current DNA and the genetic code operates (bearing in mind the fact that the epigenome operates above this code and is also inherited with continuous finer modifications, and the fact that these modifications may have been much more dramatic, rapid and profound during earlier evolutionary development as strongly indicated from the scientific literature which will become clearer as we proceed).

By peeling back the coded onion and working our way down to the level (scale) of the crystal code itself, and maybe even go a little deeper than this, this will help us to identify and assess the entire spectrum of scaled complexity operating. So beginning with our first and most complex level, when we think of DNA, it boggles the mind how such a system could itself have evolved.

However, if we try to not get distracted by all the details of complexity and look for simpler versions of forms of the DNA molecules, then we can begin to see the underlying principles that are common to more primitive (less specialised and presumably earlier scales of complexity) versions of the system.

The following excerpt just scratches the surface of the outer layers of genetic scales of complexity. It is taken from a science paper on ancestral pre-cursers to DNA is highlighted in the slightly different chemical composition of a more primitive version of DNA molecule known as TNA.

The TNA world that came before the RNA one

  Once it was recognised that DNA is key to the molecular self-replication that underpins life, chemists have sought to understand the origins of this double-helical molecule in that primordial age. It was quickly assumed that RNA, a single-stranded nucleic acid, may have been the precursor genetic material to DNA, and the RNA world hypothesis was born. But what gave rise to RNA? Chemists in the US are starting to home in on another nucleic acid, TNA: threose nucleic acid. ..

Bradley (2012, 8th January)


Another article exploring this recent discovery of the TNA molecule expands a little upon the interesting properties of this molecule in terms of an ancestral (more primitive) form of DNA and its key features of self-organisation, (self-assembly – fold into meaningful shapes via molecular bonding) and replication is given below:

Did an Earlier Genetic Molecule Predate DNA and RNA?

One approach to identifying molecules that may have acted as genetic precursors to RNA and DNA is to examine other nucleic acids that differ slightly in their chemical composition, yet still possess critical properties of self-assembly and replication as well as the ability to fold into shapes useful for biological function…

According to Chaput, one interesting contender for the role of early genetic carrier is a molecule known as TNA, whose arrival on the primordial scene may have predated its more familiar kin. A nucleic acid similar in form to both DNA and RNA, TNA differs in the sugar component of its structure, using threose rather than deoxyribose (as in DNA) or ribose (as in RNA) to compose its backbone.

The TNA world that came before the RNA one…

Threose, which has one fewer carbon atoms than ribose, is simpler than RNA not because it has fewer atoms, but rather because it can be synthesised from a single starting material,’ explains Chaput. . The researchers have now demonstrated that these selected TNA molecules can fold into complex shapes with discrete ligand-binding properties.2 Fundamentally, the work demonstrates a property of TNA that was not clear before the team began but was known, of course, in RNA and DNA. ‘This provides evidence that TNA could have served as an ancestral genetic system during an early stage of life,’ Chaput tells Chemistry World.

Astrobiology (2012, 13th January)


Now, this begins to reveal at least three scales of genetic complexity that are all built upon the previous system, starting with TNA, a more complex molecule: RNA and finally our more familiar DNA: the most complex of them all. The other important point within the above article excerpts relating to the TNA as a DNA precursor is that it works from simpler systems and builds upon these whole systems operating at a more primitive level to essentially do the same thing in more complex and later systems. And this is exemplified in the fact that TNA, apart from having lesser carbon atoms than ribose (RNA constituent), but it could be synthesised from a single starting material to get going.

This clearly demonstrates how Nature tends to start with simpler processes and then elaborates upon these recipes according to the ingredients available such as molecular complexity of sugars used. In other words, Nature seems to have evolved systems (that are ancestral to all) building upon the principle of earlier versions on increasing scales of complexity. But in order to begin understanding this level of complexity, even at the TNA scale, we need to go a little deeper still and see some of the systems that may have led to the coded complexity of life that brought it to the TNA level in the first place. I will therefore, briefly introduce you to some of the main players of the whole genetic system, if you are not already familiar with the whole system, via the review below:

How Do Genes Work

… each gene is really just a recipe for making a certain protein. And why are proteins important? Well, for starters, you are made of proteins. 50% of the dry weight of a cell is protein of one form or another. Meanwhile, proteins also do all of the heavy lifting in your body: digestion, circulation, immunity, communication between cells, motion-all are made possible by one or more of the estimated 100,000 different proteins that your body makes.

But the genes in your DNA don’t make protein directly. Instead, special proteins called enzymes read and copy (or “transcribe”) the DNA code. The segment of DNA to be transcribed gets “unzipped” by an enzyme, which uses the DNA as a template to build a single-stranded molecule of RNA. Like DNA, RNA is a long strand of nucleotides.

The Tech Museum of Innovation (2013)


We may therefore, be looking at different recipes and increasingly elaborate processes involving several players that have specialised functions in the present form of the genetic system. And as you can see, proteins and special proteins (enzymes) do the lion’s share of the work, once the DNA code (recipe) is unzipped, transcribed/translated.  Therefore, if RNA existed as a precursor to DNA and even RNA may have had a precursor and more primitive and direct interpretative system in relation to proteins, it might be useful to investigate proteins a little further within the context of the cell.

Protein Structure

Proteins are the end products of the decoding process that starts with the information in cellular DNA. As workhorses of the cell, proteins compose structural and motor elements in the cell, and they serve as the catalysts for virtually every biochemical reaction that occurs in living things. This incredible array of functions derives from a startlingly simple code that specifies a hugely diverse set of structures.

In fact, each gene in cellular DNA contains the code for a unique protein structure. Not only are these proteins assembled with different amino acid sequences, but they also are held together by different bonds and folded into a variety of three-dimensional structures. The folded shape, or conformation, depends directly on the linear amino acid sequence of the protein.

… Within a protein, multiple amino acids are linked together by peptide bonds, thereby forming a long chain. Peptide bonds are formed by a biochemical reaction that extracts a water molecule as it joins the amino group of one amino acid to the carboxyl group of a neighboring amino acid. The linear sequence of amino acids within a protein is considered the primary structure of the protein.Proteins are built from a set of only twenty amino acids, each of which has a unique side chain. The side chains of amino acids have different chemistries…

Nature Education (2014)


What is particularly interesting about the above excerpt, as it might apply to the nested scales of complexity model, is that proteins would appear to have their own direct, primary code (even though the modern genetic system now triggers and codes for these protein templates) that gives them their unique identity and function. It is also interesting that at one stage in evolutionary terms, DNA didn’t exist, and RNA did, while at another level, RNA may not have existed and only the simpler system of TNA existed and something similar in terms of coding must have existed before that. The only clear candidate is the amino-acids with their ability to chemically bond (memorise these bonds – recall the previous discussion in chapter two and Turing’s Model of the chemical basis of Morphogenesis and cellular differentiation?) and it may therefore, be simply a matter of scale.

As noted above, it is amino-acids which give proteins their primary structure and seems to point to an evolutionary preserved condition and therefore suggests a more primitive coding system (an amino-acid code perhaps) for shape, form, organisation and function of the protein system that emerged from environmental factors triggering chemical bonding sequences that remembered, a bit like memory foam?

 It is this potentially more primitive and direct coding system of amino-acids that, in its most direct and primitive form, provided the primary information of ‘How to Build a Protein’ where, the DNA now does this in a fairly indirect way and on several levels, seemingly, using all of the elements of amino-acids, enzymes, proteins, cellular functions, biochemical and molecular sequences, DNA code, epigenetic processes adapted to run the fully optimised and efficient genetic system we recognise today.

Visual account of protein investment in cellular functions

Proteins and, by extension, genes perform numerous biological functions ranging from the catalysis of chemical reactions to the formation of physical cell structures and the processing of environmental signals.

Liebermeiste et al (2014, 8488)


If we excluded the reference to genes from the above excerpt and substituted it with a sequence of bio-chemical bonds, and taking into account the bio-chemical and context dependent epigenetic system that also operates above and beyond this essential coding, we could say that the system of producing differentiated proteins, each with their own little string of amino-acid code, expressing the underlying amino-acid code according to environmentally-triggered and adaptive responses, is a self-contained environmentally sensitive primitive genetic/epigenetic coding that co-evolved within the context of the cells and itself is a precursor to the TNA/epigenetic-type coding system.

For instance, the key point of the excerpt below is that proteins possess the same fundamental properties of self-organisation as does DNA, RNA or TNA.

Protein Self-Organization: Lessons from the Min System

One of the most fundamental features of biological systems is probably their ability to self-organize in space and time on different scales. Despite many elaborate theoretical models of how molecular self-organization can come about, only a few experimental systems of biological origin have so far been rigorously described, due mostly to their inherent complexity. The most promising strategy of modern biophysics is thus to identify minimal biological systems showing self-organized emergent behavior.

Loose et al (2011, Abstract)


This article goes on to describe the best and least complex examples that they thought useful to experimentally assess, being a particular type of protein (noted in the title) which self-organises according to its environment. To reiterate this fundamental property of proteins to self-organise according to their environment and to memorise their state (not essentially requiring DNA code to form themselves into meaningful shapes), the excerpt below highlights these differential behaviours of enzyme/proteins below in an article entitled: Scale-free flow of life: on the biology, economics, and physics of the cell

Ambiguity in protein localization, interactions, structure, and function

Taking into account the fact that a protein’s conformational landscape depends on environmental context and on the protein’s own state (e.g., posttranslational modifications), one can envisage that different environments and different protein states may elicit different “behavioral routines” in the same protein. In other words, it is very likely that any given enzyme/protein possesses, in fact, a whole repertoire of context- and state-dependent behavioral routines rather than a single routine, the repertoire that has been “hard-wired” into protein structural dynamics as a set of useful sequences of coupled conformational transitions selected and “remembered” in the course of the co-evolution of a given enzyme/protein and its host.

Kurakin (2009)


If proteins can seemingly arrange and shape themselves and make connections in space and time depending upon the context and interactions as they begin to assemble themselves, just as the cells themselves appear to do via their own biochemical switching program and remember their state, then, it could be suggested that proteins within the context of the cells are forerunners or a more primitive systems of genetic memory conservation and the interface between the outside and inside biochemical world, pattern sequence formation and epigenetic imprinting.

It is also of interest that proteins form families or networks of their own kind as you will see in the next article excerpt and this is perhaps akin to the cellular families that can be triggered into becoming differentiated neurons, bone, and the soft-tissue cells in direct response to environmental factors via chemical diffusion/fusion systems discussed in the previous chapter. Are we looking at differentiated proteins just like their differentiated cellular kin? Is this another scale of the primitive genetic whole system? Recall that the differentiation of cellular families is epigenetic in nature (it operates above and beyond the coded sequence of genes and expresses them differentially).

What Are Protein Families?

All proteins bind to other molecules in order to complete their tasks, and the precise function of a protein depends on the way its exposed surfaces interact with those molecules. Proteins with related shapes tend to interact with certain molecules in similar ways, and these proteins are therefore considered a protein family. The proteins within a particular family tend to perform similar functions within the cell.

Proteins from the same family also often have long stretches of similar amino acid sequences within their primary structure. These stretches have been conserved through evolution and are vital to the catalytic function of the protein. For example, cell receptor proteins contain different amino acid sequences at their binding sites, which receive chemical signals from outside the cell, but they are more similar in amino acid sequences that interact with common intracellular signaling proteins. Protein families may have many members…


Proteins are built as chains of amino acids, which then fold into unique three-dimensional shapes. Bonding within protein molecules helps stabilize their structure, and the final folded forms of proteins are well-adapted for their functions.

Nature Education (2014)


This system (amino-acid chains and molecular bonding to form unique families of proteins), could have easily been the precursor system of the cellular differentiation according to biochemical processes described in the previous chapter. In many ways, the protein/amino-acid system provides a genetic precursor to even TNA as although it may have a different chemical composition: essentially it possesses the crucial properties of self-assembly with its ability to fold into useful shapes for biological function and these states are triggered environmentally, are context dependent and can be memorised and these critical properties seemingly operate at all scales as indicated below.

 Self-Assembly at All Scales

Self-assembly is the autonomous organization of components into patterns or structures without human intervention. Self-assembling processes are common throughout nature and technology. They involve components from the molecular (crystals) to the planetary (weather systems) scale and many different kinds of interactions. The concept of self-assembly is used increasingly  in  many  disciplines,  with  a  different  flavor  and  emphasis  in each… In dynamic self-assembly […] the interactions responsible for the formation of structures or patterns between components only occur if the system is dissipating energy.

The patterns formed by competition between reaction and diffusion in oscillating chemical reactions […] are simple examples; biological cells are much more complex ones. The study of dynamic self-assembly is in its infancy. We define two further variants of self-assembly. In templated self-assembly […] interactions between the components and regular features in their environment determine the structures that form.  Crystallization  on surfaces  that  determine  the  morphology  of the crystal is one example […]; crystallization  of  colloids  in  three-dimensional  optical fields  is  another  […].  The characteristic of Biological self-assembly […] is the variety and   complexity   of   the   functions   that   it produces.

Whitesides and Grzybowski (2002, p. 2418, ‘Science Magazine’ 29th March)


Apart from the obvious reference to the self-organising ability (and memory imprinting) of crystalline structures (which we will return to in relation to Cairns-Smith’s model further on) and the reference to the diffusion system well-known in chemistry and applied in Turing’s model for cellular differentiation as outlined previously, the information within the article referenced above, goes into the many different means by which natural systems can self-organise. To simplify this, I suppose the best way perhaps of describing how natural non-living systems can self-assemble, is that we could say there is a polarity between ‘N’ and ‘S’ of a magnet and certain particles would be attracted, or not attracted and orientated and arranged accordingly (iron filings in the presence of a moving magnet would be self-assembled).

Now to apply this to biological self-organisation using one example, we could equate this to biological cells as we know that cells have little polar-type attractors and non-attractors which relate to water-loving molecules and water-hating molecules (hydrophilic and hydrophobic respectively). Because of this property, cells do amazing things. It is a little like oil and water, where the oil in water will form whole droplets to avoid getting wet; so obviously, the oil is full of hydrophobic molecules which are more like the oily lipid membrane that protects the inner watery cellular environment that has seemingly been conducting chemical catalyst – bonding and chain building as well as molecular synthesis experiments for a very long time to get as sophisticated as cells are today.

As for coding, we could say that this can be understood, even at its most primitive and simple scale as akin to our modern use of the binary code system for computer languages. Binary code is simply ‘0s’ and ‘1s’ but look how much code can be written from the arrangements and ordering of this code. It is either on or off/activated or not. For instance, in the biological or magnetic system, every negative is a non-bond ‘0’ and every positive polarity is a positive bond ‘1’ or ‘on’ or ‘off’, which would be a foundational and simple code. However, if we bring the ability to memorise these ‘on’, ‘off’ coded sequences, into the equation, eventually, molecules will find each other a lot quicker and these chemical reactions and diffusions will get very efficient at firing together if they are triggered into doing so, akin to Turing’s biochemical ‘On’, ‘Off’ switching.

The article excerpt above: Self Assembly at All Scales, demonstrates that self-assembly is observable within many natural systems at a molecule level, so it is not surprising that chemical bonds of attraction or non-attraction can eventually form chains of bonds that in turn, build proteins or become special proteins (macro-molecules) that self-assemble (or self-fold three-dimensionally according to temperature, negative or positive polarity etc) as you will see below, proteins have very similar characteristics to cells and their building blocks: the amino-acid chains have their own code.  The article excerpt below is rather technical and long, but I thought it was worth highlighting so that you get an idea of the protein/amino-acid system and its code.

Introduction to protein structure and structural bioinformatics

The 20 Amino Acids and Their Role in Protein Structures

The amino acids are put together into a polypeptide chain on the ribosome during protein synthesis. In this process the peptide bond, the covalent bond between two amino acid residues, is formed. There are 20 different amino acids most commonly occurring in nature. Each of them has its specific characteristics defined by the side chain, which provides it with its unique role in a protein structure. Based on the propensity of the side chain to be in contact with polar solvent like water, it may be classified as hydrophobic (low propensity to be in contact with water), polar or charged (energetically favorable contact with water).

The charged amino acid residues include lysine (+), arginine (+), aspartate (-) and glutamate (-). Polar amino acids include serine, threonine, asparagine, glutamine, histidine and tyrosine. The hydrophobic amino acids include alanine, valine, leucine, isoleucine, proline, phenylalanine, tryptophane, cysteine and methionine. The amino acid glycine does not have a side chain and is hard to assign to one of the above classes.

However, glycine is often found at the surface of proteins, often within loops, providing high flexibility to these regions. Proline has the opposite effect, providing rigidity to the protein structure by imposing certain torsion angles on the segment of the polypeptide chain. The reason for these effects is discussed in the section on torsion angles. These two residues are often highly conserved in protein families since they are essential for preserving a particular protein three-dimensional fold…

…Most protein molecules have a hydrophobic core, which is not accessible to solvent and a polar surface in contact with the environment (although membrane proteins follow a different pattern). While hydrophobic amino acid residues build up the core, polar and charged amino acids preferentially cover the surface of the molecule and are in contact with solvent due to their ability to form hydrogen bonds (by donating or accepting a proton from an electronegative atom).

Very often they also interact with each other: positively and negatively charged amino acids form so called salt bridges, while polar amino acid side chains may form side chain-side chain or side chains-main chain hydrogen bonds (with polar amide carbonyl groups). It has been observed that all polar groups capable of forming hydrogen bonds in proteins do form such bonds. And since these interactions are often crucial for the stabilization of the protein three-dimensional structure, they are normally conserved.

Karadaghi (2015)


What is of particular interest here, I believe, is that when we look for the precursor system of protein/cellular and amino-acid/TNA/RNA/DNA coding system, this brings us right down to the level/scale of Cairns-Smith’s clay crystals in solution hypothesis and the inherent self-organising properties embedded within it. We have looked at self-organisation principles, self-patterning/folding and chemical/molecular bonds in response to environmental factors and interactions and ability to memorise (akin to memory foam) patterns, bonds and connections and how these might equate with the crystalline coding with modification pattern of growth and development, but we haven’t yet looked at another key feature of the crystal code within cellular structures which is clearly inherent in biological cellular systems and that is self-replication.

 It is actually quite difficult to pin-point this characteristic within biological life, but we can infer that as crystalline formations can replicate, with slight modification, from their parent matrix/lattice, a daughter formation that can grow and break off, thus cloning itself, that this method may underpin a more complex and more sophisticated means of reproduction seen within living systems today. So it may be useful to go back as far as possible on the borderlands of life itself, and  see what we can deduce about replication beyond (and on a more complex scale) the inert crystalline patterns that may have given their cue to first life.

Virus Structure

All viruses contain nucleic acid, either DNA or RNA (but not both), and a protein coat, which encases the nucleic acid. Some viruses are also enclosed by an envelope of fat and protein molecules. In its infective form, outside the cell, a virus particle is called a virion. Each virion contains at least one unique protein synthesized by specific genes in its nucleic acid. Viroids (meaning “viruslike”) are disease-causing organisms that contain only nucleic acid and have no structural proteins. Other viruslike particles called prions are composed primarily of a protein tightly integrated with a small nucleic acid molecule.

Davidson (2015)


As indicated above, in many ways, proteins are actually akin, albeit seemingly a much more primitive and potential precursor to the modern type cell, and have become a major part and function of the cell itself. Well, in the context of viruses, this primordial code-carrier dressed in a protein sheet, may be significant. The key characteristic of viruses is that they are the great replicators and are not that dissimilar in function to computer viruses, as they don’t have the ability to replicate and make lots and lots of copies of their own code and little programs to spread virally outside the context of your computer any more than biological viruses being effective outside the context of the modern cell.

But I have to say that Nature’s viruses are actually not all bad and indeed, viruses are seemingly essential to life and life itself would not have evolved much further if viruses hadn’t have developed such a cozy (symbiotic) relationship with cells. Or, it could be suggested that viruses being made of essentially the same stuff as primitive cells (chain of code and a protein sleeve for protection) are a more mobile version of the cells themselves.

For instance, some researchers prefer a cellular metabolism first hypothesis and have come up with ingenious means of how this could have occurred under natural conditions. Others have suggested the virus first hypothesis, but based upon the model used here, I would be inclined to see the viral coded critters protected by a protein sheet as a whole system which later became another scaled-up level of complexity of the whole system and some versions of that cellular/metabolic and amino-acid coding and primitive protein system became mobile (what we would call a free-living virus, which thankfully doesn’t seem to exist any longer, but this may not have always been the case – see below.

Could Giant Viruses Be the Origin of Life on Earth?

The ancestors of modern viruses may have laid the groundwork for cellular life as we know it

In the world of microbes, viruses are small—notoriously small. Pithovirus is not. The largest virus ever discovered, pithovirus is more massive than even some bacteria. Most viruses copy themselves by hijacking their host’s molecular machinery. But pithovirus is much more independent, possessing some replication machinery of its own.

Pithovirus’s relatively large number of genes also differentiated it from other viruses, which are often genetically simple—the smallest have a mere four genes. Pithovirus has around 500 genes, and some are used for complex tasks such as making proteins and repairing and replicating DNA.

“It was so different from what we were taught about viruses,” Abergel said

Arnold (2014, ‘Quanta Magazine’ 17th July)


However, present-day viruses seem to be fairly restricted and only effective in the context of cells and this seems to be therefore, a fairly fixed symbiotic relationship. And as you will see in the final chapter of this book, viral-like mobile remodelers of the genome in times of stress, means that viruses may have been major players in the fact that we are here at all.

We can begin to see how Nature may have used the systems and materials to produce scaled up variations on the same fundamental theme and to form these as whole systems from the ground up. Mobile non-cellular viruses (but made of the same stuff) and cellular colonies co-evolving in a symbiotic relationship perhaps? Take for example, the scaling from amino-acids, to more complex molecules such as TNA, RNA and finally DNA, protected by flexible and environmentally sensitive protein rings (segments) and we can begin to see how and perhaps why, the code cannot operate outside the context of the cell and vice-versa. This co-dependent, environmentally-driven system leading to modification of the code itself, becomes even more intriguing when we explore another key feature of viruses, namely the fact that they are assembled from a two-dimensional crystalline structure as outlined in the excerpt below.

Two-dimensional crystalline structure assembled from outer shells of a virus

In a paper published in Soft Matter, September 2013, scientists announced their discovery of a two-dimensional crystalline structure assembled from the outer shells of a virus. A virus consists of a protein shell protecting an interior consisting of either DNA or RNA.

“We are excited about the potential of virus-like particles as building blocks for creating new nanostructures,” said the paper’s lead author, Masafumi Fukuto, a physicist in the Condensed Matter Physics and Materials Science Department at Brookhaven National Laboratory. “For the particular virus that we studied, we discovered two new forms of 2D crystals that are distinct from previously observed hexagonal and square crystals.”

Rowe (2012,’Physics.Org’ 21st February)


As seemingly, amino-acids are the primary (primordial) code and assembled (chemically-bonded by natural organising properties of these molecular systems at all scales) and their outer protective coat of the proteins with their own organisational properties according to polarities etc, we now have a further clue to the sophistication of this holistic and symbiotic system in terms of the crystalline nature of the protein/coding system itself. The underlying crystalline nature of this system is further supported in the next section where just about everything in the body, from the proteins in your eye lens, to whole protein systems, and from DNA and the formation of the double helix is crystalline.

We could be seeing the emergence of the software and the hardware required to carry out fundamental coding (chemical bonding, chemical ‘on’, ‘off’ switching, which have all the hallmarks of the more developed coding and cellular system allowing for macro-molecular synthesis via special proteins – enzymes etc); and we now have the basis of an environmentally sensitive and controlled system for the reproduction/replication of the primary coding format in the form as a crystalline organism itself – as seen in the virus-type entity.

The gives us an insight into how the crystalline hypothesis can be taken to a completely distinct new, but related level, as you will see in the following section. This is where the whole system would appear to take an unexpected quantum leap in crystalline complexity and perhaps it is this level of sophistication that makes it alive as you will see below.

Quantum Liquid Crystalline Life

From the most fundamental properties embedded within clay-crystal in solution, we can begin to see how Cairns-Smith’s theory may work, particularly, if we understand it as a more primitive, scaled-down version of the whole cellular/genetic/epigenetic coding system. For instance, at a highly evolved level and on a larger scale of the whole system, proteins and their crystalline structure is no better exemplified by those found in your eyes. See below:

Soon, sight-saving treatment to protect eyes from cataract

It has long been known that human eyes have a powerful ability to focus because of three kinds of crystalline proteins in their lenses, maintaining transparency via a delicate balance of both repelling and attracting light.

ANI (2013, ‘Zee Health News’ 6th December)


Furthermore, the powerful efficiency of liquid crystals as a highly responsive information system and the source of coordinating a whole organism with its patterning and structural properties, is strongly indicated in the following excerpt and points to the ability of these crystalline properties of, and within cells. Note that LCLCs stand for lyotropic chromonic liquid crystals.

Scientists to Advance Biology-Liquid Crystal Research

Liquid crystals represent the fourth phase of matter…

Certain organic materials exhibit the liquid crystalline state as they transition between the solid and the liquid states, known as mesophases. Though liquid crystals are best known for their application in displays, they also are an essential part of all life. Liquid crystals in organisms include the amphiphilic lipids of cellular membranes, the DNA in chromosomes, all proteins, especially cytoskeletal proteins, muscle proteins, collagens and proteoglycans of connective tissues. These adopt a multiplicity of mesophases that may be crucial for biological structure and function at all levels of organization, from processing metabolites in the cell to pattern determination in development, as well as the coordinated locomotion of whole organisms.

Kent State University (2005, ‘’ 11th October)


As noted above, the liquid crystal phase is also important to DNA in the chromosomes which, is elaborated upon in a little more detail in another science excerpt below:

Liquid crystalline phases of ultra-short DNA and RNA sequences

The ability of long, hydrated, double-stranded DNA to form liquid crystal phases has been known for more than 50 years and played a key role in the initial deciphering of its structure…Recent collaborative work between the Boulder group and the Complex Fluids and Molecular Biophysics group of the University of Milan has shown that self-pairing, or complementary, DNA oligomers as short as six base pairs can exhibit chiral nematic and columnar LC phases …

Zanchetta and Nakata (n.d)


The chiral pairs they are talking about refer to right or left-handedness, meaning the orientation of how structures line up. So therefore, the more recent data is pointing to very powerful memory systems and ordering of molecular sequences – not to forget the ability of these molecules to fold in meaningful ways and self-organise and perhaps this begins to give us an insight into the shape and form of the double helix structure of the DNA code itself. This is described below.

Polymers and Liquid Crystals

chiral molecule

A molecule that is not identical to its mirror image. This gives a chiral substance its characteristic twisted shape, due to the fact that its molecules do not line up when combined.

cholesteric liquid crystals

    Also known as Chiral Nematic. Similar to the nematic phase, however, in the cholesteric phase, molecules in the different layers orient at a slight angle relative to each other (rather than parallel as in the nematic). Each consecutive molecule is rotated slightly relative to the one before it. Therefore, instead of the constant director of the nematic, the cholesteric director rotates helically throughout the sample. Many cholesterol esters exhibit this phase, hence the name cholesteric…

cholesteric mesophase

    Nematic liquid crystals with chiral centers form in two dimensional nematic-like layers with directors in each layer twisted with respect to those above and below so that the directors form a continuous helix about the layer normal.

Case Western Reserve University (2004).


This suggests an explanation for how the distinct double helix structure with its meaningfully arranged molecules may have bonded. This twisted ladder effect as a property of certain liquid crystalline behaviour in solution is indicated in the excerpt below. It also begins to give you an insight into the more dynamic properties of self-organising, shaping/forming and patterning within solution with different polarities (context dependent) when observed within certain liquid crystals.

Liquid Crystal Droplets gemstones

In a study published in the Proceedings of the National Academy of Sciences, researchers from the University of Pennsylvania and Swarthmore College describe new research into a type of liquid crystal that dissolves in water rather than avoids it as do the oily liquid crystals found in displays. This property means that these liquid crystals hold potential for biomedical applications, where their changing internal patterns could signal the presence of specific proteins or other biological macromolecules.

The researchers placed these liquid crystals into water droplets, which in turn were placed in oil, producing an emulsion. At high enough concentrations within the droplets, the liquid crystals exhibit a twisting pattern visible under an optical microscope.

Lerner (2014, ‘Phys.Org’ 21st January 21)


In other words, this information above regarding the polarity of cellular/protein and their crystalline properties in particular liquid solutions and at specific quantities, under certain conditions, can be extrapolated to infer that the metaphase transition (of liquid crystals) allowed for a high level of fluidity and structure to propel the whole genetic system within the context of the cell to coordinate itself into living organisms.

And the main driver may have been informational where, the cellular system – the flexible hardware was itself a little organelle (miniature functional part of a cell) and responsive enough to adapt to varying environmental conditions and in turn, update the software accordingly. Basically, the cells and code working together (not forgetting the epigenetic code), in a feedback loop between organism and environment with the ability to remember, replicate and adapt and pass on the new information.

The information aspect of liquid crystal systems is seemingly the key to understanding this process and must be understood in the context of the crystalline properties and behaviour of proteins and cells in general. The crystalline coding system is exemplified in the short excerpt below, even though it is discussing a technological application of liquid crystal information storage systems, it may be relevant to our discussion of Nature’s crystalline information system.

Liquid crystals light way to better data storage

As cell phones and computers continue to shrink, many companies are seeking better ways to store hundreds of gigabytes of data in small, low-power devices.

A special type of liquid crystal, similar to those used in computer displays and televisions, offers a solution. Unlike CDs and DVDs, which store information only on their surface, lasers can encode data throughout a liquid crystal. Known as holographic storage, the technique makes it possible to pack much more information in a tiny space.

American Institute of Physics (2010,  ‘ScienceDaily’24th June)


Nature doesn’t have lasers as far as we know, but light can be focussed differentially from natural light frequencies in different spectrums and this we are all familiar with in the form of photosynthesis used by plants. We could suggest from all of the above that as exemplified in the proteins in the cells of the eye and their liquid crystalline properties, that this is a good clue to how Nature may have focussed light in a similar way to arrange molecules as information storage systems, presumably prior to cellular colonies becoming whole coordinated cellular organisms.

As suggested all along and indicated above and as you will see below, with regard to protein liquid crystalline behaviour, the genetic code cannot be seen in isolation to the protein and/or cellular system. Therefore, if we now look at the cell itself with its self-similar properties of ordering and meaningful structuring in direct relation to its interactions and biochemical/molecular environment, polarities in solution and temperature, we can gain an insight into the fundamentals of the whole interactive system.

Lipids and Membrane Structure

Membrane fluidity: The interior of a lipid bilayer is normally highly fluid (…). In the liquid crystal state, hydrocarbon chains of phospholipids are disordered and in constant motion.

At lower temperature, a membrane containing a single phospholipid type undergoes transition to a crystalline state in which fatty acid tails are fully extended, packing is highly ordered, and van der Waals interactions between adjacent chains are maximal.Kinks in fatty acid chains, due to cis double bonds, interfere with packing of lipids in the crystalline state, and lower the phase transition temperature. Cholesterol, an important constituent of cell membranes, has a rigid ring system and a short branched hydrocarbon tail. Cholesterol is largely hydrophobic. But it has one polar group, a hydroxyl, making it amphipathic is the ability…

Rensselaer Polytechnic Institute (2015)


Now when you hear about taking care of your cholesterol levels and taking your fatty-acids, you might think differently about what this actually means. This excerpt also brings to mind the discussion of the oil and water type attraction and repulsion system (polarity and charge) or the water loving molecules and those trying to avoid water, working much like a magnetic field, akin to the Morphogenetic field well known by its effects to anyone studying cellular and embryological development? As the excerpt above outlines, the liquid crystalline behaviour is very much context depend. .

The all-important behavior of certain proteins is further explored in the excerpt below in terms of the liquid crystalline properties and the fundamentally similar behavior and equally context dependent nature of cells and the fundamental properties of the code itself. However, when this next article talks about mutants, they mean a change occurring from a different solution (environment). Although quite a difficult science paper to follow, it does highlight a few key points about proteins and their underlying self-organised amino-acids (there are only 20 combinations and these are ubiquitous on the planet and beyond – apparently).

The self assembly of proteins; probing patchy protein interactions


This work suggests a mechanism by which protein …interactions can be probed in a systematic manner. This type of data is critical if good molecular models to predict protein behavior are to be developed. .., we created a protein, which forms two different crystal types, one that melts when the solution is heated and one that melts when the solution is cooled, with co-existence of the two crystal forms at 303 K, the point at which the individual liquidus lines for the single mutant variants overlap.

This observation is unprecedented. On a broader level, this work is a starting point which will require a combination of further experiments and complementary simulations to more clearly understand the interplay between the complex, competing forces controlling protein self-assembly and crystallization. However, it is clear that the surface characteristics of the protein, defined by the surface amino acids, can lead to a variety of condensed phases for the same protein. A change in the external environment, e.g. temperature, results in some amino acids contributing more to the protein self-assembly behaviour than others, leading to the variety of structures that we observe.

James et al (2015, 5419)


What I believe is most significant from the point of view of the nested scales of complexity model as it is employed throughout this present book, is that the article excerpt above states that it is clear “that the surface characteristics of the protein, defined by the surface amino acids, can lead to a variety of condensed phases for the same protein” which directly reflects the nested doll principle, where the surface features of the more primitive amino-acid system informs the main characteristics of the next level up: proteins.  It is the spaces in between the nested dolls that give us the most information, rather than getting distracted by all the detail of variations from these interactions that lead us in the wrong direction when trying to peel back the scaled layers of this genetic onion.

As discussed in Chapter Two (see preview of 1st five chapters), we know that cells, particularly pluripotent cells (unprogrammed), are highly sensitive to their environment/temperature/chemical landscapes and that this can cause a chemical chain reaction that programs the cells to become differentiated. Therefore, looking at evolution in terms of levels and scales of complexity, it is perhaps not that surprising that, proteins and at another scale: enzymes are similarly sensitive to their environments and interactions with each other and this can inform their shape and form and ultimately function. On another scale, this mirrors the crystalline growth system and with the added phase transition and dynamically responsive and fluid system of liquid crystalline growth and development we now have the foundation for speciation (the differentiation of the pluripotent) organisms themselves.

The self-assembly properties are therefore, seemingly, a complex interplay of molecular interactions in solution and at different temperatures, proteins surface interactions and differential polarities and tensions and memory bond via natural attractors or polarity factors than bind particular chemicals/molecules leading to self-assembly at an atomic level and later (on another scale), a chemical and then molecular and macro-molecule scale. This complex interplay between the interactions such as the liquid crystalline condensed phase and a very dynamic system indeed as you will see below, leads us back to the idea that D’Arcy Thompson proposed that the most interesting discoveries are to be made on the borderlands of disciplines, where one science meets another as discussed in Chapter One. Similarly, the excerpt article above indicates that it is the interplay of the different forces on the borderlands of amino-acid and protein surfaces in the context of their environment that creates dynamic and very interesting results.

This of course brings us to the scaled up version of cellular systems and its interplay with the coding system and the organisms themselves. As we have been going from the bottom up and scaling each of these systems all the way, it is natural to see if the dynamic fourth phase of matter of the crystalline system: liquid crystal phase, is actually in evidence during the latter stages of embryological development or indeed, after the cellular differentiation stage. Indeed, as seen below, there is evidence to support the important role of liquid crystal phase during an organism’s development.

The study below is by MengMeng Xu and Xuehong Xu (Affiliations: Duke University School of Medicine, Department of Physiology Centre for Biomedical Engineering Technology, Centre for Stem Cell Biology and Regenerative Medicine, University of Maryland Medical School and Shaanxi Normal University School of Life Science, USA/China).

The patchy history of this much neglected area of this type of fascinating research is outlined below in the introduction, followed by the more recent conclusions based upon a number of studies. There is a little bit of scientific terminology which may not make a great deal of sense, but the main idea from this article is that there is very good support for the presence of the liquid crystal stage (dynamic phase transition) during early development (embryogenesis) and I have presented it here to reiterate the fact that all of these interacting systems appear to have co-evolved in relation to environmental factors and interactions, that it is reflected at every scale of life and this has implications for how the species itself came into being in the first place.

Liquid-Crystal in Embryogenesis and Pathogenesis of Human Diseases

In  1979,  a  systematic  publication  summarizing  the  state  of  research  on  liquid-crystals  in biological organisms was published [Brown GH et al  1979]. After this historic publication on liquid-crystals and biology, the field remained largely dormant for more than two decades. However in 1978 and 1979,  Haiping  He  and  Xizai  Wu,  who  had  continued  pursuing  this field  despite  international  disinterest,  reported  their  findings  on  liquid-crystal  involvement  during  chicken  development.  For the first time, they revealed that  massive  quantities of liquid-crystals in the liver, yolk sac, blood, and many other developing tissues and organs of chicken  during  embryogenesis.  Their later studies also reported similar liquid-crystalline structures during fish development.

In 1988, another group reported the existence of vaterite CaCO3  within  the  liquid-crystals  found  in  yolk fluid,  identifying  the  spherical  calcified structures  first  reported  in  1979  as  one  of  three  iso-forms  of  calcium  carbonate  [Feher  G  1979,  Li  M et  al  1988]. Subsequent studies have identified liquid-crystalline structures to be omnipresent in the liver during avian development [Xu XH et al 1995a, 1995b, 1997]. Recent studies have  revealed  that  liquid-crystals  play a  critical  role  in  the  preservation  of  calcium and  other  trace  elements  required  for  embryo  development  [Xu  MM et  al  2009,  2010,  2011; Xu XH et al 2009, 2011a]…

General characteristics of embryonic liquid-crystal

 During embryogenesis, liquid crystals are widely distributed in the tissues of vertebrates and invertebrates,  including  Apis  cerana  chrysalis, fish,  reptile,  avian  and  mammal  early  embryo  in  vitro  [X  XH  et al  1993, 2009, 2011a, Xu MM et al 2009 2011]. In chicken development, more than  twenty  different  organs  and  tissues  exhibit  liquid  crystal  droplets  including  liver,  meso and  metanephros,  lungs,  blood  in  heart,  and  brain.  The presence of  liquid  crystal  normally appears  at  different  developmental  stages  depending  on  the  tissue  type,  and  lasts  until  early postnatal stages. The earliest liquid crystal droplets appear on the inner embryonic disc during the second day of development [He H et al 1978].  Regardless of their distribution, however, the liquid crystal droplets  eventually  vanish  within  three  to  four  weeks  into  the  postnatal period, also depending on tissue type maturation [X XH et al  2009, 2011a]…


Based   on   current   discoveries   obtained   via   XRD,   SAXS,   confocol   microscope,   and polarization microscopy in combination with cryo-section, push-release procedure for fluidity measurement, and thermal stage for phase transition progress has been made in the field of liquid crystal function in embryogenesis and pathogenesis of human diseases. With this  methodology,  the  research  has  proved  that,  during  the  embryo  development,  liquid crystals  are  readily  identifiable  in  the  embryo  through  their  Maltese  Crosse  birefringence texture.  Liquid crystals with this configuration display strong fluidity accompanied with shape-changing   properties   under   direct   pressure   conditions.

Xu and Xu Xu and Xu (2012, 637, 643 and 649)


This much neglected field of study became a focus for the research of Mae-Wan Ho who began to take a multi-disciplinary approach as you will see below, and discusses the process of Morphogenesis and pattern formation (recall Turing’s model of the Chemical Basis of Morphogenesis). According to the excerpt above, and the following excerpt, Ho and her collaborators certainly do seem to have discovered the most interesting phenomenon on the borderlines or the interface between different fields of science (just where D’Arcy Thompson said we would find the most interesting answers). The science paper is entitled: Organisms as Polyphasic Liquid Crystals, in Bioelectrochemistry and Bioenergetics 41, 81-91, 1996 [83] and its authors are: Mae-Wan Ho, Julian Haffegee, Richard Newton, Yu-ming Zhou, John S. Bolton and Stephen Ross and reflects the collaboration between the fields of biology, bio-electrodynamics and physics and the sub-field of quantum mechanics to name but a few.

Liquid crystals and pattern determination

One of the first generalizations to emerge from developmental biology is that early embryos and isolated parts of early embryos show a strong tendency to form whole organisms. This gave rise to the notion of a morphogenetic field – a spatiotemporal domain of activities organized globally to form the whole organism…

At the start of embryogenesis, the morphogenetic field exhibits ‘pleuripotency’ or ‘totipotency’, where all parts has the potential to develop into any structure. In the course of early embryogenesis, however, determination occurs in which the different parts of the embryo become more and more restricted in their developmental potential. The determined state can be demonstrated by transplantation and grafting experiments. If a piece is removed from an embryo before determination and transplanted to a different location, or grafted to another embryo, then the piece will develop in harmony with its surroundings. If the same experiment is carried out after determination, the graft will develop into the structure it was determined to be, irrespective of its surroundings. Thus, the graft may develop into a limb on the back of the host, for example. The process of determination was discovered a century ago, but its basis remains largely unknown despite impressive advances in the molecular genetics of morphogenesis in recent years.

The significant feature of pattern determination is that the determinative influences not only possess dynamic field-like characteristics, but are material and transplantable. …

A vital clue to the basis of determination may have been provided by Totafurno and Trainor (…) who successfully interpreted classical experiments on transplanting and grafting limb-buds in salamander, in which supernumery limbs were often induced, in terms of a non-linear vector field. This vector-field is precisely the sort that is embodied in liquid crystal phase alignments. … liquid crystals go through in transitions from the liquid to the solid state, which are comparable to the successive stages of determination of the limb-buds in amphibians…

There is indeed a wide range of liquid crystalline mesophases from the most dynamic and liquid – possessing orientation order in one dimension without any translationnal order – to the most solid – with orientation order in 3-dimensions and also a large measure of translational order. It is conceivable that in the course of development, the relevant liquid crystalline mesophases do undergo transitions from the dynamic and fluid to the relatively more (meta)stable, patterned regimes…

Ho et al (1996, Liquid Crystals and Pattern Formation)


More of this research can be found in the book, noted above and entitled: The Rainbow and the Worm: The Physics of Organisms (2008, extended 3rd edition) by Mae Wan Ho [84]. Essentially, Mae-Wan Ho, from her deep research and experimental work and observations, led her to propose that the liquid crystalline phase and its high precision and holistic resonant molecular ordering during Morphogenesis, could be explained in terms of quantum coherence, a well-known phenomenon within the tiny atomic world describable by quantum mechanics and its intrinsic link to another branch of physics which studies the dynamic properties of the liquid crystalline complexity as seen in her talk below. Her observations also dovetail with and are pertinent to the study outlined earlier by Xu and Xu (2012) [85].

What it means to be Quantum Coherent

Quantum coherence and the liquid crystalline “rainbow worm”

The “rainbow worm” is this little fruit fly larva I first encountered in 1992 as it was hatching from its egg. We placed a batch of eggs in a continuously irrigated chamber on a microscope slide under the polarizing microscope and waited. The microscope was set up so we can see the organism developing and getting energized, right through to the arrays of molecules that make up its tissues and cells. …But what do the colours mean?

Geologists use the polarising microscope to identify rock crystals. We have slightly modified the setting, but the principle is the same. The rainbow colours are generated by crystals with orderly arrangements of atoms and molecules. We were puzzled at first. In rock crystals or liquid crystals outside the organism, molecules and atoms certainly have an orderly arrangement that stays ordered because there is no movement. But in the living organism nothing is static, the molecules and atoms are moving all the time. So how can they maintain the molecular order required to generate the brilliant crystal colours? …

The only explanation is that the molecules are moving coherently together, so much so that they appear as ordered as a static crystal. To cut a long story short, the molecules, especially the big ones, macromolecules like proteins and nucleic acids, thoroughly infiltrated with water, are in a dynamic liquid crystalline state. To begin with, they are completely aligned with their electrical polarities to form a continuum that links up the whole body, permeating throughout the connective tissues, the extra-cellular matrix, and into the interior of every single cell. More importantly, all the molecules, including the water, are dancing together as a whole, and the more active they are, the more coherent, hence the brighter the colour…

So, these beautiful images of living organisms are direct evidence of their high degree of coherence. And this high degree of coherence itself depends on the liquid crystalline matrix that enables every single molecule to intercommunicate, synchronize and syncopate with every other. The water, making up some 70 percent by weight of the organism, is the most important part of the living liquid crystalline matrix, without which it cannot form. Many molecules, DNA and proteins, would not be stable; and would not function without water; water is also crucial for the intercommunication that enables the organism to work as a coherent, perfectly coordinated whole […] …Mainstream biology has steadfastly ignored the liquid crystalline organism and all its implications.

Ho (2008, ‘Institute of Science and Society’ 1st October)


Mae-Wan Ho’s theory becomes even more compelling when we understand that Nature, apparently, has been using quantum coherence – a well-known phenomenon described by quantum mechanics – for a very long time. This quantum aspect of cellular life has apparently been sitting under our noses all this time. For instance, it is positively “jaw-dropping” says Johnjoe Mc Fadden (working on the quantum nature of Nature) in a recent article seen in Discover Magazine entitled: Solving Biology’s Mysteries Using Quantum Mechanics.

 “Physicists had been battling for years to build a quantum computer — and now it seemed that all that time they may have been eating quantum computers for lunch, in the leaves in their salad!”

Merali (2014, ‘Discover Magazine’, 2th December)


One key principle of the quantum world is that the word quantum itself basically means a discrete packet with irreducible parts – i.e. it is all about whole systems and it is a tiny world as otherwise things get too noisy and busy for the quantum effects to operate. This is elaborated upon and echoes some of Mae-Wan Ho’s conclusions in a science paper in the Journal of Physics conference papers (2011) by Seth Lloyd in the following:

Quantum Coherence in Biological Systems

Nature is the great nano-technologist. The chemical machinery that powers biological systems consists of complicated molecules structured at the nanoscale and sub-nanoscale. At these small scales, the dynamics of the chemical machinery is governed by the laws of quantum mechanics. Quantum mechanics is well known to exhibit strange and counterintuitive effects. Accordingly, it makes sense to investigate the extent to which peculiarly quantum effects such as coherence and entanglement play an important role in living systems. Quantum mechanics and quantum coherence play a central role in chemistry. Quantum coherence and entanglement determine the valence structure of atoms and the form of covalent bonds. Quantum mechanics fixes the set of allowed chemical compounds and sets the parameters of chemical reactions. Indeed, the very fact that there are only a countable, discrete set of possible chemical compounds arises from the fundamentally discrete nature of quantum mechanics. Chemistry, in turn, lays down the rules for what biological structures are possible and for how they function. Biomolecules can contain many atoms (billions in the case of DNA). As molecules become larger and more complex, quantum coherence becomes harder to maintain. Vibrational modes and interactions with the environment tend to decohere quantum superpositions. Consequently, most biomolecular mechanisms have traditionally been modeled as essentially classical processes…

Lloyd (2011, 1)


Therefore, once you start to become a quantum computer in Nature’s scheme of things: it seems that you will become the best quantum computer possible, as you are not just one giant complex cell, driven slavishly and randomly by your genetic code. You are made up of a whole fractal network of trillions of interacting and cooperative, communicating nano-scale liquid crystalline quantum cellular system. Using this ingenious system of making miniature copies of the original system of patterning and being able to continually modify the program, update it according to adaptive needs and in direct relation to the environment, is the ultimate quantum computer, and it is biological, seemingly. This brings us to Mae-Wan Ho’s discussion on quantum liquid crystalline organisms compared to our most recent attempts to develop quantum computing as outlined in the article excerpt below.

The quantum coherent organism and quantum computation

…Quantum superposition and quantum entanglement are the signatures of quantum coherence, and they have been attracting a lot of attention with regard to the possibility of a quantum computer, as opposed to the conventional classical computer now in use.

A quantum computer operates on the quantum bit or ‘qubit’ instead of the ordinary bit in a classical computer. While the ordinary bit is a simple binary 1 or 0, the qubit can hold 1, 0, or crucially, a quantum superposition of 1 and 0. In fact, it can hold anything up to an infinite number of values in superposition […] .A quantum computer can in theory do computations that are intractable with a classical computer or achieve exponential speedup in solving certain problems. And building an actual quantum computer has become the holy grail of a new breed of quantum information technologists…

To my mind, the perfect quantum computer already exists: it is the quantum coherent living organism…

Consider the elementary process of a protein folding into shape, a difficult problem even for the fastest classical computer. It takes about 300 years for a classical computer to simulate a small peptide of 23 amino-acid residues (with associated water molecules) to fold into shape. By running simulations simultaneously on some 140 000 individual computers around the world, researchers took over three weeks […]. Real proteins, however, fold to perfection in several microseconds […].

It is very important for proteins to fold correctly. Incorrect folding makes proteins aggregate into insoluble, inflexible clumps associated with wasting diseases such as mad cow disease, Alzheimer’s Diesease, Huntington’s and Parkinson’s Disease…The model of the quantum coherent organism depends on reciprocity and cooperation, rather than relentless Darwinian competition as in the mainstream model …

Hopefully, this is a new paradigm that will support a new world order that’s much closer to how nature is, that will enable us to live sustainably within her…

Ho (2008, ‘Institute of Science and Society’ 1st October)


Using this system, it is therefore perhaps not that surprising that life got so complex, but it is quite astounding that we may now be looking at quantum evolution that is a polar opposite and several billion light years from our current Darwinian model. Furthermore, now having used the Matryoshka principle to look at the coding system at every possible scale, maybe we should begin taking a salad leaf out of Nature’s recipe book and use this to build our future technology in accordance with hers. At least the nano-technologists are beginning to recognise this, perhaps the biologists will begin to catch up – but I’m afraid they will have to let go of their pet theory first or they will completely miss the point.

For instance, I came across an excerpt which seems to be at least looking in the right direction. It is a bit technical, but hopefully, you’ll get the idea. The solution would appear to be those liquid crystals again and I like their idea of scalability:

Nuclear magnetic resonance quantum computing using liquid crystal solvents

Liquid crystals offer several advantages as solvents for molecules used for nuclear magnetic resonance quantum computing (NMRQC). The dipolar coupling between nuclear spins manifest in the NMRspectra of molecules oriented by a liquid crystal permits a significant increase in clock frequency, while short spin-lattice relaxation times permit fast recycling of algorithms, and save time in calibration and signal-enhancement experiments.

Furthermore, the use of liquid crystalsolvents offers scalability in the form of an expanded library of spin-bearing molecules suitable for NMRQC. These ideas are demonstrated with the successful execution of a two-qubit Grover search using a molecule (13C?1HCl3) oriented in a liquid crystal and a clock speed eight times greater than in an isotropic solvent. Perhaps more importantly, five times as many logic operations can be executed within the coherence time using the liquid crystalsolvent.

Yabbibu (1999, Abstract)


Final Thoughts on the Evolution of Computer Technology and its Nature’s Bio-Chemical/Crystalline System

Just as another little thought experiment, picture how the abacus was once, and indeed, still is useable as a self-contained counting system for tens of centuries before Babbage’s first computation machine or, the punch-card system used to code for the first IBM computers and the same principle of coding that allowed the great textile mills to pattern their linens and clothes, where the same design could be repeatedly produced from the same underlying pattern of a series of holes in a card, even in different factories. If one card got damaged; you could always make copies from the original or modified copies.

The telegraph system used another type of code, producing information that could be passed between vast distances; then came the telephone and we now have mobile phones. The typewriter was used mechanically and eventually we got the electric one, once we had electricity of course, but it was still a typewriter. And from the camera, to moving film and eventually sound, we all ended up with viewable boxes in our homes that we call televisions. And of course, the internet once the typewriter technology merged with the television to become your keyboard and monitor; the coded punch-cards were put on floppy discs and the computing machine became a super computing device and when the phone came into the equation and merged with the computing system, well, we know that the whole system became greater than the sum of its parts, in fact it is going quantum, yet each part was once a whole system, and you can still see whole functional systems within the greater whole. All the systems, irrespective of how primitive it may seem to us today, were once fully functioning technologies in their own right.

The main difference between this analogy and Nature is that Nature would appear to be highly efficient at using all the available resources and is the great recycler and adapter. At every level of life, even the microbial world, still have critical jobs to do. From the bottom feeders up: to ourselves and everything in between which is essentially made of stardust anyway, are part of one whole sustainable natural system. And perhaps instead of thinking of literal ancestors, i.e. the computer keyboard descended directly from the old Imperial Typewriters, and trying to find the missing link for what gave rise directly to the mouse and its imminent demise (nearing extinction apparently) and it has become an endangered species due to the superior advances of the touch-screen, we should perhaps see that the systems behind these innovations are fundamentally the same at every scale and it is this that is ancestral to them all.




The Scaled Fractal nature of Nature

William Blake

(1757 – 1827)

To see a World in

a Grain of Sand

And a Heaven in a Wild Flower

Hold Infinity in the palm of your hand

And Eternity in an hour…

-‘Auguries of Innocence’

My Fractal Journey

It all started, I suppose  now when I look back, when I was about seven years of age and standing in-line with the rest of my class (funny word to use – we don’t do grades in Ireland). It was the height of the ‘troubles’ and it was a convent school for girls right in the centre of it all. (I have given away my age and background here; perhaps a little too much). Anyway, what has this to do with my first fractal revelation?

Well, the setting is quite relevant, but the time may not be so. The room that we were all standing in was filled with lines of girls according to their age and class, and this room had a special name – ‘The Red-Room’  on account of it having a checkered patterned floor of red and pale coloured tiles. This room  should however, have been called the mirrored room as the two main opposing walls were adorned with massive gilded framed mirrors and of course, there was the expected statuette and other religious paraphernalia, along with obligatory singing high-pitched Nun vamping on the slightly discordant ivory keys (she was one of those rare fun-loving Nuns and her name was Sister Anne).

Some of you may have already guessed from the set-up, what I suddenly and profoundly came to understand – in what could only be described as a silent eureka moment;  remember, I’m only seven – so I don’t know any of this intellectually, nor do I have a language for it – at least not  until I was a very mature adult – my early education was really woefully poor – but you could say that all that I learned in that moment was good enough for anyone’s life-time and I was in school at the time.

Suddenly, everything came into sharp focus. The long sequential rows, on every scale, reflected in the opposing panes, ran to what seemed to be infinity in ever-decreasing lines of green-clad girls. Anyone who has ever studied fractals knows that self-similar patterns are reflected at scales within scales and the more you zoom into the deeper and smaller levels, you find the same type of pattern  reflected repeatedly. It’s just a matter of scale.


Mandelbrot Set Zoom CC. licence Wikimedia

I cannot put into words how profound this deep understanding of things, the world (before the usual indoctrination of how the world works according to the cultural dictates of our time) that came like an instant download in that moment. But it probably did guide me at some deeper level (after several years of research) towards an understanding of the inherent fractal nature of Nature. This brings us to one of the main players in a very distinct (non-Darwinian) but, dynamically  much more explicable model of evolutionary thinking (click on the title below for a short bio and a summary of his ideas along with some other forgotten theories of evolution in a related article on this site and/or read on for the summary of a more universal scaling fractal explanation of his concepts and how they relate to an over-arching alternative evolutionary model, which dovetails (fractally at every scale) with several other alternatives:

D’Arcy Wentworth Thompson

(1860 – 1948)



D’Arcy Thompson was born the year after Darwin published his famous book On the Origin of Species. And in 1917 D’Arcy published his own quite famous book: On the Growth and Form and much extended and updated version in the 1940s (See Thompson 1917 [link] and Thompson 1945 [Link]). In his major treatise, he uses the known processes and principles of the physical sciences of chemistry, physics etc in conjunction with biology and by applying the language and tools of mathematics, he essentially quantified and established inherent patterns of growth and form that Nature appeared to consistently use in the production of even the most complex organisms.

He essentially, came to a distinctively different way of understanding evolutionary development and ultimate complexity by applying the main principles of the processes known to operate within non-biological complex systems, to biological systems and discovering that there was something universal underpinning them all, as indicated in his 1945 edition On Growth and Form.

There is something, an essential and indispensable something, which is common to them all, something which is the subject of all our transformations, and remains invariant (as the mathematicians say) under them all.

D’Arcy Thompson (1945, 1085)

About D’Arcy
… the dynamic influence of starting conditions lies in the morphology of shells and horns. These are the permanent, non-living, three-dimensional record of a temporary, two-dimensional living state – the base of the horn, or the mantle of the shellfish. D’Arcy Thompson showed that all horn and shell morphologies could be described in simple mathematical terms readily derived from the incremental nature of growth… For instance, geometrical rules of packing determine cell arrangements. These need not be specified, but can arise spontaneously. Yet the packing arrangement may be “useful” in minimising the space occupied by the cells, by maximizing cell-cell contacts, by establishing different categories of cells (“inside” versus “outside”), and so on…

― University of Dundee and the University of St Andrews (2010)

In other words, D’Arcy Thompson’s general alternative views on evolutionary processes were in principle based upon scaling laws of fractal patterning and these universals embedded in Nature,  led him to propose and apply a very different kind of descent with modification: as summarised in the excerpts given below taken from his epilogue of the 1945 edition On Growth and Form.

Note that protozoa refer to the entire kingdom of animals, and are four-limbed animals and that this is a later edition of D’Arcy’s book (1945).

On Growth & Form
…for eighty years’ study of Darwinian evolution has not taught us how birds descend from reptiles, mammals from earlier quadrupeds, quadrupeds from fishes, nor vertebrates from the invertebrate stock…
… Our geometrical analogies weigh heavily against Darwin’s conception of endless small continuous variations: they help to show that discontinuous variations are a natural thing, that “mutations” -or sudden changes, greater or less-are bound to have taken place, and new “types” to have arisen, now and then. Our argument indicates, if it does not prove, that such mutations, occurring on a comparatively few definite lines, or plain alternatives, of physico-mathematical possibility, are likely to repeat themselves: that the “higher” protozoa, for instance, may have sprung not from or through one another, but severally from the simpler forms; or that the worm-type, to take another example, may have come into being again and again.

Thompson (1945, 1093-95, Epilogue)


In summary, D’Arcy Thompson seems to propose throughout all his chapters in relation to the main topics addressed, that biological life has followed the same fundamental processes inherent in other complex and naturally organising phenomenon and he believed that by tracing the intrinsic patterning and scale employed by Nature, we can begin to see the methods of producing continuous novel and increasingly diverse formations of shape and form that could be implicated in the great variety of species; and yet may be commonly connected by sharing underlying patterns of fundamentally similar properties and employing the same means of development to reach their own particular level of intrinsic complexity. How he arrived at his conclusions are best summarised below:

Transformations: The Visual Influence of D’Arcy Thompson
D’Arcy passionately believed in giving students as great a breadth of knowledge as possible, telling them if you dream, as some of you, I doubt not, have a right to dream, of future discoveries and inventions, let me tell you that the fertile field of discovery lies for the most part on those borderlands where one science meets another. There is a cry in the land for specialization. . . but depend upon it, that the specialist who is not reinforced by a breadth of knowledge beyond his own specialty is apt very soon to find himself only the highly trained assistant to some other man. . .
Try also to understand that though the sciences are defined from one another in books, there runs through them all what philosophers used to call the commune vinculum, a golden interweaving link, to their mutual support and interpretation.

Jarron (2013, 83-4).
Google books

For instance, as a result of more recent collaborations between physicists and biologists attempting to identify the obvious universals embedded in life (in the spirit of what D’Arcy Thompson had proposed as the most productive way to pursue scientific investigations), Geoffrey West and others have been led to discover consistent power laws, universals and invariants in Nature, along with fractal networks common at all scales and all of this phenomenon having predictable properties, led West to declare the following in the excerpts from an interview in the New York Times below:

”Everything around us is scale dependent…
It’s woven into the fabric of the universe…

It is truly amazing because life is easily the most complex of complex systems,’ …. ‘But in spite of this, it has this absurdly simple scaling law. Something universal is going on …”

Johnson (1999, ‘New York Times’ 12th January)

The video below should give you a general insight into the type of research and the findings which point to the fact that underlying all of biological complexity are, surprisingly simple universal scaling laws governing fractal-like networks.

Perhaps, I should point out at this stage, that the more recent collaborations between physicists and biologists have led to the re-evaluation and acknowledgment of D’Arcy Thompson’s work and contributions to revealing the deeper complexity of biology, but they seem to take the cautionary approach to stating these laws and invariants of scale and form in more general and less emphatic terms than D’Arcy Thompson did as indicated below. They also do not go as far as re-assessing our current model of evolutionary complexity in the light of these findings as D’Arcy Thompson was prompted to do (but perhaps they don’t know about the fundamental flaws in our existing paradigm in the first place). If you are in any doubt, I would suggest reading the link to the readable quote book here , it’s a flip book and reads just like the real thing and see what an increasing number of well-respected scientists thing about the science behind the Darwinian form of evolution, particularly our modern synthesis):

Life’s Universal Scaling Laws
Although few today would articulate Thompson’s position so provocatively, the spirit of his characterization remains to a large extent valid, despite the extraordinary progress during the intervening century. The basic question implicit in his discussion remains unanswered: Do biological phenomena obey underlying universal laws of life that can be mathematized so that biology can be formulated as a predictive, quantitative science?
Most would regard it as unlikely that scientists will ever discover “Newton’s laws of biology” that could lead to precise calculations of detailed biological phenomena. Indeed, one could convincingly argue that the extraordinary complexity of most biological systems precludes such a possibility. Nevertheless, it is reasonable to conjecture that the coarse-grained behavior of living systems might obey quantifiable universal laws that capture the systems’ essential features. This more modest view presumes that, at every organizational level, one can construct idealized biological systems whose average properties are calculable.

West and Brown (2004, 36)

Therefore, we could go one of two ways here and either acknowledge that even in the light of our more modern approaches to trying to understand biological complexity, D’Arcy Thompson’s model is still highly relevant; albeit as an idealised concept and useful for grasping the essence of biological systems and how they appear to work. On the other hand, we could take the position that D’Arcy Thompson took, based upon a much broader approach to the most up-to-date evidence from many fields of study and apply them to biological systems and restate his universal patterning of life in terms of biological laws that hold at every level in Nature – This is the underlying principle – The fractal Nature of Nature; the apparent driver and the underpinnings of the non-random directional change and the principle that makes meaningful and highly efficient forms, shapes and patterns in nature. See first five chapters of forthcoming book (needs final edit) to get an idea of how all this fractal scaling applies to biological complexity and by inference evolution.

final backcover info for evolution book one

In the aforementioned book, the scientific evidence has led to me taking the latter approach and as you will see: his dream of placing biology en par with the mathematical descriptions afforded physics and chemistry really do appear to hold across the entire spectrum and at every scale of life. They are quantifiable and predictable, not just descriptions of life, but a key to unlocking many of its mysteries embedded in the evolutionary process itself. In my mind, this is good science, as these laws and equations of scale can be tested and applied to find out things we could not otherwise directly measure.

For instance, by looking to fundamental properties within naturally developing non-biological complex systems, where, under certain conditions, rapid and profound changes can be brought about via catalysing the whole system in a single leap, D’Arcy Thompson applied this principle to evolutionary development and suggested that whole functional cellular life and its highly organised organisms could have come into being likewise a number of times under broadly similar catalytic conditions. He also understood that a very small change (initial starting conditions) at the beginning; can make a huge difference further down the line, reflecting yet another fundamental characteristic of natural complex systems. This led him to suggest that primitive life could have been triggered into taking fundamentally divergent paths by simply having different starting conditions.

D’Arcy Thompson suggested that as several distinct groups were discernible, based upon his study and observations of quite distinct body-plans and internal systems of a broad range of species, that these may represent the resultant divergent forms alluded to above. He referred to these distinct groupings of organisms as “discontinuous types”, meaning that Nature drew upon their underlying form and inherent systems to produce many scaled-up and increasingly complex versions of the same fundamental forms “Types” with degrees of modification according to the group’s intrinsic evolutionary potential.

Who Wrote The Book of Life?
Picking Up Where D’Arcy Thompson Left Off
NASA scientists are using Thompson’s biomathematical studies of life forms on Earth to postulate about life forms throughout the universe. There are certain universal conditions that will always affect the shape of a life form, wherever that life may be.”Everywhere Nature works true to scale, and everything has a proper size accordingly,” wrote Thompson. “Cell and tissue, shell and bone, leaf and flower are so many portions of matter, and it is in obedience to the laws of physics that their particles have been moved, moulded and conformed.” … Gravity, for instance, acts on all particles and affects matter cohesion, chemical affinity and body volume. Other influences that are consistent throughout the universe are temperature, pressure, electrical charge and chemistry.

NASA (1999, May 28th)

  Is the nature of Nature, simply a matter of fractal scales…?

DNA nebula molecule compared

What do you think?

Please comment, share and otherwise join me in this conversation if you are as fascinated,  as I am, by our Natural world and seek some serious answers, email me at:


Cheers Maria Brigit





Another predictable Scaling Law?

Leading on from last week’s discussion of universal scaling laws within Nature, brings us to yet another seemingly universal phenomenon; a  recurrent and predictable embedded pattern,  formulated  and traditionally associated with the experimental agriculturalist Max Kleiber. His theory relates to the apparent predictable ¾ power laws where metabolic rate and mass are plotted for a diverse range of animals (see Kleiber, 1932 – Body size and metabolism). Link

Note, that all the images used in graphs within the following charts are my addition to existing graphs and data and are used to simplify and clearly illustrate the concept of scaling.

 scales metabolismFig. 1:  Based upon the metabolic rate to mass/surface area presented by Kleiber’s ¾ scaling law. As mammal mass/surface area increases: so does its metabolic rate increase on a scalable gradient slope.

Applying Kleiber’s laws in a more modern era has proved rather fruitful and more researchers have added on anything from amoebas to antelopes since his original proposal. Everything really would appear to scale in terms of metabolic rate to mass by factors of predictable magnitude. Now there has been hot debate regarding this law and the fact that it seems to apply almost universally and there are always exceptions to the rule. However, as seen in a science paper entitled: Experimental allometry: effect of size manipulation on metabolic rate of colonial ascidians published in more recent years, this issue has been fully addressed by using actual living populations:

The allometric scaling of metabolic rate of organisms, the three-quarters power rule, has led to a questioning of the basis for the relation. We attacked this problem experimentally for the first time by employing the modular organism, the ascidian that forms a single layered flat colony, as a model system. The metabolic rate and colony size followed the three-quarters power relation, which held even after the colony size was experimentally manipulated. Our results established that the three-quarters power relation is a real continuous function, not an imaginary statistical regression.

Nakaya, Saito and Motokawa (2005. abstract),


 The ¾ law is best explained using the information provided by A Van Aken from Brighton and Sussex medical school (slide-share) entitled: Neuroscience made understandable (link) which I have paraphrased as follows: When reading these charts where (body weight) mass is plotted against metabolic rate, the chart is showing a gradient and scalable linear relationship (obeying the ¾ power laws). The numbers that you see above are transformed from the actual weights etc of different animals to a logarithmic scale. Base 10 is used in this case and the reason for this is that if you attempted to plot the actual range of magnitudes such as a mouse of less than 100 grams against elephants weight over 1000kg on same scale, these would be off the charts. Therefore logarithmic scales are used so that we can view them on the same chart. However, it does not take away from the fact that these animals when body weight and metabolism are plotted reflect the seemingly universal scaling law or the ¾ power law as seen on the gradient slope.

All in all, the same predictable properties of scale are detectable across all of Nature according to many in-depth studies since Kleiber’s time. For instance, this seemingly universal pattern of the ¾ power laws is highlighted in an interview with West in the New York Times: Of Mice and Elephants: a Matter of Scale in the following:

This relationship seems to hold across the animal kingdom, from shrew to blue whale, and it has since been extended all the way down to single-celled organisms, and possibly within the cells themselves to the internal structures called mitochondria that turn nutrients into energy.

—Johnston (The New York Times dated to Jan 12th 1999)


 Although, the ¾ power law applies to animals ranging from microbial life to elephants as will become clearly apparent as we proceed, West and Brown encountered a problem which arose when they attempted to apply the same ¾ scaling law to the very different world of plants. This is important to mention, as we are attempting to find universals for evolutionary complexity itself, but I also point to this issue to demonstrate how science should work as exemplified in a study undertaken by West et all and illustrates that when physicists get it wrong, as they occasionally do: they admit it and go back and pose different questions and keep investigating. This is taken from the  same interview article as above: Of Mice and Elephants: a Matter of Scale:

 What emerged closely approximated a so-called fractal network, in which each tiny part is a replica of the whole. Magnify the network of blood vessels in a hand and the image resembles one of an entire circulatory system. And to be as efficient as possible, the network also had to be ”area-preserving.” If a branch split into three daughter branches, their cross-sectional areas had to add up to that of the parent branch. This would insure that blood or sap would continue to move at the same speed throughout the organism. The scientists were delighted to see that the model gave rise to three-quarter-power scaling between metabolic rate and body mass. But the system worked only for plants.

”We worked through the model and made clear predictions about mammals,” Dr. Brown said, ”every single one of which was wrong.”

In making the model as simple as possible, the scientists had hoped they could ignore the fact that blood is pumped by the heart in pulses and treat mammals as though they were trees. After studying hydrodynamics, they realized they needed a way to slow the pulsing blood as the vessels got tinier and tinier. These finer parts of the network would not be area-preserving but area-increasing: the cross sections of the daughter branches would add up to a sum greater than the parent branch, spreading the blood over a larger area. After adding these and other complications, they found that the model also predicted three-quarter-power scaling in mammals. Other quarter-power scaling laws also emerged naturally from the equations. Evolution, it seemed, has overcome the natural limitations of simple geometric scaling by developing these very efficient fractal-like webs.

—Johnston (The New York Times dated to Jan 12th 1999)


At least these scientists were willing to ask the right question using their multidisciplinary tools of enquiry. Anyway, they figured it out in the end and this gives us a much better understanding of how the same laws apply across all species, but that Nature has sometimes made adaptations to these systems to work at their optimum level according to resources and it would appear to do it using fractal networks. The nature of fractal-like patterning and the rules of growth and development reflect the scaling concepts of D’Arcy Thompson’s research (Link to Article) discussed a few weeks ago on this site. There is seemingly, a common underlying (universal) principle that guides growth and development, no matter what the species and these fractal-like networks relating to the efficiency of the biological systems (in energy exchange with their environment) seems to be the cause that gives rise to predictable scales of complexity and results in our measurements consistently showing the ¾ power law.

For instance, these fractal networks operating within actual organisms (species) are outlined in functional terms and in terms of the same fundamental system operating within species as diverse as mammals, fish and plants in the following in the Universal Review:

Mammals have richly branched air tubes, but they are confined to special organs, the lungs. Fish do a similar thing with gills. Trees use their richly dividing branches to supply their leaves with water and pump sugars back from the leaves to the trunk. The 3/4-power law is derived in part from the assumption that mammalian distribution networks are “fractal like”…


 Recall that D’Arcy Thompson’s observations  led to the identification of the common underlying principles of scale and the fact that everything grows in near perfect proportion to itself via repeating patterns on every scale (reiterations) (Link to Article). For instance, there may also be a reason why our five fingers don’t sprout five smaller fingers at the tips of our existing one. This may be because everything is a whole system within a larger whole system, just at different (repeating patterns) scales of complexity.

Again, it would appear to be all about the efficiency of the whole system in relation to everything else. This is perhaps why we don’t have five digit extremities and not many continuous branching and ever decreasing multiple miniature digits, apart from the fact that they would look ridiculous and you would fall over a lot, it simply would be a very efficient way of getting blood circulating and everything else that you need around the whole body.


Fig. 2: ‘freaky-fractal-fingers’ from article in Live Science

However, a tree would put on continuous branches reflecting the ratio of distance of the previous branches and the overall shape of the tree itself and the veins of some leaves can be seen to form this same branching pattern, on ever decreasing scales. But, even the tree will eventually stop branching and just consolidate what it has, growing thicker and maturing (stabilising phase in the universal growth curve – see last week’s article) according to its natural life cycle and the resources available within the context of the whole forest.

To emphasis this further, the following explanation for these principles of scale according to efficiency of the whole biological system is given in The Theory of allometric scaling laws in biology from genomes to ecosystems: towards a quantitative unifying theory of biological structure and organization, by Geoffrey B. West and James H. Brown.


… all organisms share a common structural and functional basis of metabolism at the molecular level. The basic enzymes and reactions are universal, at least across the aerobic eukaryotes. Additional general rules based on first principles determine how this molecular-level metabolism is supplied and regulated at higher levels of organization: from organelles, to cells, to organisms, to ecosystems. The most important of these rules are those relating to the size of the systems, including the body size of the individual organisms, and the temperature at which they operate. Our theory of quarter-power scaling offers a unified conceptual explanation, based on first principles of geometry, biology, physics and chemistry for the size-dependence of the metabolic process. The theory is based on generic properties of the metabolic distribution networks in simplified, idealized organisms.

West and Brown(2005, Introduction)


In other words, this is a shared generic system across seemingly most species that have been studied, albeit in an idealised form (physicists tend to see the bigger patterns – the invariants and don’t get bogged down in the details), but it does produce predictable results which are always worth paying attention to in science, they do conform to first principles established in several fields.  Although cells look and behave very differently to microbes and mice are very different to men, there is an underlying commonly shared system that relates to energy exchange between the organism and its environment.

There are other predictable properties that emerge when studied from the fractal perspective such as the heart beats on average throughout the life cycle of an average mouse will scale in the same ratio to that of an elephant and the smaller animal has faster beats, but the scale according to their mass heart rates in mammals showing the ¾ power law of scaling as pointed out in Allometric Relations and Scaling Laws for the Cardiovascular System of Mammals by Thomas H. Dawson Link

As indicated above, West and others have established these scaling laws for a wide range of biological phenomenon, however, their research also shows that they apply to other systems such as the growth of cities to the fractal-like nature of the communication networks and the growth of corporations; just about anything and everything systems (See last week’s article on this site). This is interesting as the Sigmoidal growth curve applies similarly to these ‘manmade’ systems as discussed in last week’s article on the topic. According to these researchers, it is all about distribution of resources which by their very nature forms fractal-like (space-filling) networks, whether the system is directly biological or run by biological entities (See Life’s Universal Scaling Laws, by West and Brown) Link and for more information on these broader scaling laws follow this link to view a video [You Tube] where Geoffrey West gives a very good lecture on the topic, see Scaling Laws In Biology And Other Complex Systems (2012) Link

There is definitely something universal going on if, as these scaling factors apply to anything from small business to big corporate entities and from the rail network to the whole infrastructure that supports big cities that started out as a one horse town, there is a universal growth/evolutionary pattern emerging.  And of course biological systems are not that different as they are all about distribution of resources as well. Below are some examples of related biological phenomenon that scale predictably and follow the ¾ power law, but with a slight twist which gives support to D’Arcy Thompson’s alternative evolutionary scenario of fundamental types and diversification from these generalist types that create all the variations that we call a species.

For instance, another predictable phenomenon identified within biological systems is the concept that small organisms reproduce (multiply/replicate) much faster than larger organisms. Basically, as most of know from common knowledge, a small species like a mouse reproduce very fast compared to larger mammals such as elephants. This is referred to as intrinsic rate and it means that there is an intrinsic difference between the reproductive capacities over time according to size of the organism. Mammals for instance with a self-regulating metabolic system- homeothermic, (warm-blooded) is rather different to a virus, but viruses predictably scale in relation to mammals in terms of their intrinsic rate being 100,000 times greater than a mammals! Essentially, as we know the rate and mass/size of one organism, we can predict according to size, the proportions or intrinsic rate in this case of any organism.  See chart below:

scales metabolism intrinsic rate

Fig.  3:  Chart based upon rate of increase in relation to mass/weight of organism. Note the discrete groupings of fundamental forms/types with only a slight overlap between the more complex animal groups (Diagram based upon figure 11.21 Body size and intrinsic rate of increase – data from Fenchel 1974, Link)

Again, the scaling is very clear where all organisms tend to fall within the predictable slope (gradient) according to their mass/size (fundamental metabolic type) and rate of increase in this case.  These are discrete groups of organism where the bacteria are quite distinct from virus organisms and protozoa (small animals that we can’t see for the most part) are a whole metabolically distinct group that in turn only overlap slightly with cold-blooded animals such as fish, amphibians, reptiles and these are a discrete, and only slightly overlapping group/type with the warm-blooded mammals and birds.  Another simplified chart which plots metabolic rate to mass is illustrated below. Here the discrete groupings of very different organisms are clear as well as the fundamental leaps (discontinuous lines) of metabolic complexity.

scales metabolism animals

Fig.  4:  Chart based upon metabolic rate to mass for diverse organisms ranging from unicellular to cold-blooded invertebrates and vertebrates and from warm-blooded vertebrates. Again note the discrete groupings of fundamental forms/types seemingly nested in scales of complexity.(Chart based upon data from  Link and Tatsuo Motokawa, “Elephant’s Time, Rat’s Time” Link

The charts for intrinsic rate for groups of major life-forms from singled-celled  organisms, to cold-blooded and warm-blooded species, clearly cluster into discrete metabolic groups and the leaps of metabolic complexity between each group is worth drawing attention to. In other words, the neat continuous grade seen exclusively for mammals is not the case when we plot these ratios for organisms with distinct metabolic systems, beyond warm-blooded mammalian forms. This might not seem that amazing at this stage, but it does give us a big clue to evolutionary development, which will become much clearer as these articles on alternative evolution continue. It begins to support D’Arcy Thompson’s fundamental types or archetype forms from which divergences can occur.

For instance, by employing the power laws of metabolism to mass, intrinsic rate to mass and other things such as heart rate to mass, we wouldn’t be top of this evolutionary tree metabolically speaking – elephants and whales are because they are bigger mammals than ourselves. Their mass and the fractal-like networks (space-filling needs) would be scaled up proportionately to make the metabolic system (the heat/energy exchange between the organism and its environment) work at optimum level. But as mammals, we out-rank in complexity of our warm-blooded metabolic system, the cold-blooded (simpler) vertebrates such as lizards and amphibians and in turn they out rank fish and fish outrank insects and so on and so forth, if you want to talk in competitive terms.

But, Nature would not appear to be this linearly hierarchical – it is fractal and each part is related to the whole on self-similar scales of complexity and therefore the relationship between the different species may be less literal and not so much about direct common ancestral descent, or as D’Arcy Thompson proposed, not through each other progressively as the Darwinian model would follow, but  from a common underlying patterning with many divergent and distinct forms which we would refer to as species. They share the same systems for patterning, growth and form and now it seems metabolic to mass ratio fractal patterning as well.

Just to reiterate the importance of the discrete fundamental types of species are trying to tell us about evolution, I do find it interesting that a mouse-sized lizard cannot be plotted within the higher scale of metabolism with a mammalian mouse of the same size, but remains fundamentally at the level of metabolic complexity seen in present-day lizard species. Does this mean an invariant? Is this an indication of a fundamental archetype form from which all divergent patterns on the same theme emerge into species as proposed by D’Arcy Thompson? In other words, the species may become fundamentally fixed (stabilised) once they reach the optimum level of their innate complexity and are metabolically in balance with their environment. The book entitled: Evolution, if it wasn’t by Darwinian means, how did it happen? goes into much more detail on this where is much scientific evidence to support this concept (See  main menu of this site under ‘BOOKS’ for more information).

These fundamental forms and their discrete groupings based upon metabolism, another chart, again based upon ratios of mass to metabolism is given below. It is shows the scaling exponents of fish, amphibians, reptiles, birds and mammals (which I have represented literally to illustrate the point with images) and is based upon the actual results of a study by White et al (Abstract 2006). Interestingly, this study disputes the scaling laws as they sometimes show non-universals and it is these differences that are actually quite revealing from the perspective taken here.

scales metabolism fundamental types

Fig.5:  Chart of the fundamental ‘types’ of species that scale according to radically distinct metabolism according to their mass within discrete groups. (chart is based on figure 1 from White et al 2006,

Note that West and others have adequately addressed such criticisms raised by White et al who have proposed heterogeneous scales or scales that don’t exactly conform to the ¾ power rule.  Now, as the chart clearly shows, birds and mammals are discretely grouped and basically fall within the gradient of their own slope and are therefore distinct from cold-blooded animals as they are more akin based upon warm-blooded metabolism. However, although all the groups follow a scaled slope according to mass and rate of metabolism, each group or archetype: fish, amphibian, reptile, bird and mammal, can be seen as discrete groups and only overlap slightly with each plotted gradient within their overall group .

In combination, these charts and the scaling principles in general, strongly suggest that the name of the evolutionary game is growth and innovation according to resources. It is seemingly about fractal-like (networks) space-filling and efficiency at the end of the day.  This common metabolic system to mass in exchange with its environment would allow growth on every scale of complexity, according to available resources. In a sense, species could develop and become increasingly complex according to their intrinsic metabolic potential and expand to eventually fill every niche on the planet as long as the resources became available, which looks very likely given the type of evidence is presented  throughout the book noted above (Evolution, if it wasn’t by  Darwinian means…?).  In other words, a form of co-evolution between the species and ecological system itself seems to be occurring.

This understanding and predictable properties of these systems therefore have real potential to project back in time and try to begin understanding the growth patterns that evolution itself might have followed according to these scaling laws. D’Arcy Thompson’s framework which was based upon the universal patterns that he found within all the great diversity of life which were underlain by simple fractal-like and predictable scaling laws, he proposed from these findings that fundamental forms could diverge into many different varieties leading to what we would call a species, may actually be the case.

All in all, what D’Arcy Thompson offers by way of this alternative evolutionary scenario of species going from fundamental unspecified types (generalists) to multitudes of divergent and differentiated forms (specialised species) according to natural laws of scale and form which can be described mathematically, as outlined in previous articles, is beginning to find much support as you will see as we proceed. I will just finish up this article with a quote from D’Arcy Thompson’s book On growth and form and you will find it quite pertinent to the next article (coming shortly on this site) focussing on the lesser known contribution to evolution theory from Alan Turing who is more commonly known in association with early computers and mathematics and his significant contribution to cracking the Enigma Code of WWII. Alan Turing also helped decipher another code  in biology and its wasn’t DNA, but rather the chemical switches that turn genes on or off and in particular ways during development – in his theory of Morphogenesis. Below is D’Arcy Thompson’s pertinent quote:

And while I have sought to shew the naturalist how a few mathematical concepts and dynamical principles may help and guide him, I have tried to shew the mathematician a field for his labour- a field which few have entered and no man has explored…For the harmony of the world is made manifest in Form and Number, and the heart and soul and all the poetry of Natural Philosophy are embodied in the concept of mathematical beauty.

Wentworth-Thompson (1917 Epilogue)


Everything Grows (evolves?) according to the universal growth curve

Continuing on from last week’s focus on D’Arcy Thompson’s alternative evolutionary understanding – universal scaling laws, which are finding strong scientific support in more recent times, particularly within the field of physics and its application to biological systems, as noted previously: D’Arcy Thompson’s belief that a broader approach to the bigger questions would produce  exciting, predictable patterning in Nature that can be summarised in powerful, yet simple equations, is coming to pass.

”Everything around us is scale dependent,’’…

”It’s woven into the fabric of the universe.”…

  ”It is truly amazing because life is easily the most complex of complex systems,’ …. ‘But in spite of this, it has this absurdly simple scaling law. Something universal is going on.” …

—Johnson (New York Times Jan 12th 1999)

   This brings us to the other dimension of Growth & Form which D’Arcy Thompson explored: Time in relation to growth. Indeed, D’Arcy discussed such patterns of non-linear and predictable patterns of natural growth and development in his extended (1942) edition of his book: On Growth & Form Link

Once, again these universal predicable scales of magnitude continue to be in evidence everywhere we look. Perhaps D’Arcy was actually on to something fundamental about biology.

 The Universal Growth/Evolution Curve

For example, West draws attention to yet another fundamental invariant – the universal (or almost universal) growth curve in the following:

…Still largely missing, however, is a theoretical framework for understanding the mechanisms that affect whole-organism growth trajectories. So questions such as why growth curves are almost universally sigmoidal, what controls the final or mature body size, and what affects the allocation of energy and materials to growth and development remain largely unanswered.

 sigmoidal simplified growth curve.jpg

Fig. 1:  Idealised chart showing the Sigmoidal growth/evolution over time curve. Left-hand section shows typical ‘Lag Phase’, the centre section where ‘S’ (Sigmoidal curve) rises rapidly and is sometimes referred to as the ‘Exponential Phase’ and finally, the third section (right) is the slow growth/evolutionary stage at the top of the ‘S-Curve’ which could be described as the ‘Stablisation Phase’.

 This is seemingly the pattern followed by everything that we have observed and recorded growing or developing, colonising or multiplying in the natural world or systems created by us, follow the Sigmoidal growth pattern as seen in the evolution of internet, computer technology and even social media platform such as Facebook as presented in simplified (idealised) form in the diagrams below.  Therefore, it is seemingly – universal and we should therefore pay attention to this pattern to see if we can establish how evolution itself evolved (growth and development at another scale and level of complexity. For instance, the things that we can observe and study in real time where, the Signoidal growth pattern is clearly the pattern commencing with a lag phase (fairly slow coalescence of all the necessary aspects needed to create the next level of the whole system), followed by an explosion of growth (an exponential phase) and finally a leveling out of growth and stability with further refinements of the existing system (or organism) – filling out the detail.

This Sigmoidal growth pattern can be seen in the slow development of a woodland, to later (exponential) colonisation of an area and finally, stability. See example below in Figure 2.

scaling seedling

Fig. 2: Sigmoidal growth/evolution over time curve applies to the growth of a seed to a sapling to maturity. Plant biomass is Sigmoidal (See:

.scaling trees

Fig.3:  Sigmoidal growth/evolution over time curve applies to the growth of an entire woodland. (See figure 11.5  Exponentlal growth of a colonizing population of Scots pine. Pinus sylvestris. Data from Bennen 1983.

From the seed to the sapling and from the mature plant to the entire colonisation and biomass, follow the same Sigmoidal growth pattern from a lag, exponential and stabilisation stage. The growth of yeast populations and their colonisation are no different, their growth rate is much faster, but this is relative to and proportional to their scale (size).

scaling yeast

Fig.4:  Sigmoidal growth/evolution over time curve applies to the growth of colonies of yeast. as seen in: figure 11.8 Sigmoidal growth by a population of the yeast Saccharomyoces cercvisiac . Data from Gause 1934 Or bacterial colonies is also Sigmoidal, but will rapidly decline in closed system such as a Petrie Dish (See:

Embryological development has a lag phase, quickly followed by an exponential growth phase and stabilisation – it is one again Sigmoidal. And I could fill a page with all the other instances, in other words, biological growth and development and even evolution is predictably Sigmoidal. Basically, as Thompson proposed: at every scale and level, things grow proportionally and in a predictable manner and can therefore be used to calculate otherwise unknown things in nature. This is the beauty of the mathematical formula.

scaling embryo

Fig.5:  Sigmoidal growth/evolution over time curve applies to the development and growth of an embryo. Then the embryos grew up to develop social media and the internet that also followed a lag phase, an exponential phase and finally reached maturity and stablisation.
scaling facebood
Fig.6:  Sigmoidal growth/evolution over time curve applies to the growth of social media: facebook being one well-known example.

What makes the Sigmoidal curve, not only important as a model for seemingly all natural systems that grow and evolve, from the internet (see above illustration of facebook, a successful mega-social media forum on the internet, which may be obsolete by the time you read this, if it hasn’t ground to a slow stabilised trickle by the time you are reading this. From cities to rail networks, as long as they continue to be required and fashions don’t change too much and from broccoli to bacteria, the Sigmoidal curve applies. However, biological life has apparently found a way of not becoming easily extinct, unlike our ‘manmade’ systems, and indeed, life has seemingly learned to beat the law of entropy (tends to disorder and decay) or become both an ‘open’ and ‘closed ‘system at the same time (look up the second law of thermodynamics). But essentially, our bodies may wear out and die, but life itself seems to go on and manage to keep doing against all the odds.

The overarching principle or growth/evolution and species formation according to natural forces that can be predicted, quantified and explained mathematically (or at least a lot of it, but certainly not all – such as the very beginning of it all – but it has tried and that is the topic of another book in the making), forms a major part of the larger evolutionary puzzle which will only probably make more sense when we have applied all that follows and much of what has been said already to the fossil record in Part Two of the forthcoming book: Evolution: If it didn’t Happen by Darwinian means, how did it occur?

D’Arcy Thompson’s model of evolutionary change (which forms Chapter One of the forthcomming book and initiates Part One, the alternative scientific explanations of evolutionary processess, which collectively form a natural distinct synthesis),  proposed that the eloquent underlying cohesion of Nature and biological life is discoverable and predictable at all magnitudes (scales) and therefore can be applied to trying to figure out the processes of evolution itself.

As the Sigmoid growth/evolutionary curve appears to be a universal (or almost universal as noted above by West), it is therefore not perhaps that surprising that it could possibly reveal things that we couldn’t otherwise know about Nature, such as the tempo of evolution itself.  For instance, the Sigmoidal universal gives us a clue the tempo and pattern of life and therefore an insight into evolution itself may have occurred, if it wasn’t by Darwinian means as for example, the ‘S’ Curve also clearly shows us the tempo of life in the Pre-Cambrian period (the lag phase), the explosion of life itself (the exponential phase) and finally, the stabilisation of the species as a whole (stabilisation).

It even looks like the Sigmoidal growth equation could be applied to the embryological development and reflect on a smaller scale, the greater Sigmoidal tempo of the development (evolutionary) of the species itself, as indicated within the alternative evolutionary model presented in Chapter Three of the forthcoming book and the fourth part of this present series within this blog.

The possible reason for all Natural things (and systems created by Natural things) being Sigmoidal, with an initial lag phase, followed by an exponential phase and then stabalisation, may never be understood, but seemingly it is the most efficient, time and space-saving way. As, seemingly, Nature abides by natural laws of area/space filling rules in relation to energy concerns and available resources (which is fractally definable/measurable), as the work of West and others suggests.

Follow this link to view a video [You Tube] where Geoffrey West gives a very good lecture on the topic, see Scaling Laws In Biology And Other Complex Systems (2012) Link

 The seemngly universal pattern of growth and development according to the Sigmoidal growth (evolutionary?) curve and a very simple equations, that being universal, should therefore, apply at every scale of life, as we have observed it for all other scales that can be quantified.  In principle, therefore, the pattern that evolution itself and the formation of the species should be knowable, eventhough, we do not a have an actual time machine to go back and observe the dramatic eruption and incredible adaptive moulding and shaping of life, we can at last begin to make more than a guess based upon assumptions, that are firmly grounded in true scientific understanding and application.

Everything seems to be a tiny whole system from its origin and reflected at every scale and magnitude and embedded within a larger whole system. This is a fractal system of self-similar repeating (reiterating) patterns at every scale. One pattern reflects the whole.

Here is a little thought experiment. Forget everything you have ever been told about evolution – Try, I know it is very difficult….Think of the principle of Russian Nested Dolls and how the very small (unformed and less defined) origin doll is made from the same materials and directs the scaled up form of the next  leap of complexity. Nature will seemingly continue to grow more complex versions of the same fundamental form according to available resources. She would appear to cut her cloth to her measure (the old axim used to refer to tailors) and like an expert nested doll maker, each form is sculpted (shaped and formed) according to well established, tried and tested rules. Each increasing scale fits snuggly over the previous form, allowing more detail and complexity to be filled in and expanded upon. This is the overarching principle of the emerging concept of The Nested Doll Evolutionary Model.

nested dolls