Monday, July 17, 2006
1) Journals 2) Papers 3) Expertise 4) Donations
The day-to-day purpose of this blog (when time allows!) is to reflect ongoing research into the possibility of a testable internal evolutionary mechanism based on an extension to homeostasis (see Why research an 'Internal Evolutionary Mechanism'? and The Internal Evolutionary Mechanism: Basic Concept).
The ultimate objective being the putting together of a series of arguments designed to arouse the curiosity of someone with the resources to prove, or disprove, the proposal.
In the meantime, as an independent researcher, my own resources are limited and help in any of the following areas would be very welcome! (email email@example.com)
1) Access to Journals (JSTOR, Nature, Science, PNAS, etc.)
A few months ago I emailed Niles Eldredge about an 1889 paper by JM Clarke describing fibonacci spirals in trilobite eyes which Niles refers to in his book Time Frames (scanned here).
Unfortunately, Niles had lost track of the citation but did think the paper may have been published by American Scientist. One internet contact then searched JSTOR on my behalf while others provided details of trilobite papers which might be of interest.
The activity was spread over two weeks at the end of which the wanted paper still hadn't been found. Many such quests come to a (hopefully temporary) halt but it would be so much faster - as well as maintaining 'continuity of research' - if I were able to access resources directly.
Individual authors have been very helpful in responding to requests for copies of papers.
When direct approaches aren't possible it can be quite good fun using Google to track down papers 'hidden' in obscure regions of cyberspace. Overall, however, this is very much a hit-or-miss approach and it doesn't help when such papers are subsequently moved or deleted! (although they are sometimes 'retrievable' via archive.org).
Two areas where help is required immediately spring to mind:
a) Help in developing a mathematical analogy of the proposed internal evolutionary mechanism - see the flowchart in The Internal Evolutionary Mechanism: Basic Concept). I also need advice on analysing matrices, specifically this one: Cytochrome C and species divergence
b) I would be very interested in hearing of phenomena such as those described in Info wanted on two intriguing 'Lamarckian' experiments (email)
Until I win the lottery and am able to hire the services of a fully-equipped lab (not that I'm holding my breath!) donations will be offset against the cost of books/papers/subscriptions/etc..
Secure transactions via PayPal can be made by using the "donate" button at the top of the sidebar, or email for alternative methods of making a contribution.
John Latter / Jorolat
(Support/Sponsor 'Evolution Research')
technorati tags: internal+evolutionary+mechanism, evolution, research, sponsor, support, publications, books, papers, journals, jorolat, john+latter, paypal
Thursday, March 23, 2006
Comment: Symmetry and Asymmetry
This news item reminds me of the Palmer papers on symmetry and asymmetry in the Main Blog:
"Snails with left-handed shells can have a big advantage in life - predators may find it impossible to eat them.
That is the conclusion of research just published in the Royal Society's journal Biology Letters.
Scientists from the US examined whelks and cone shells preyed on by the crab Calappa flammea.
They found the crab is unable to open left-handed shells because it only has a tool for peeling them on its right claw; so it discards them.
'The crabs have a special tool on their claw, a tooth that's used like a can-opener,' said Gregory Dietl from Yale University.
'So, if you imagine trying to use a right-handed can-opener with your left hand - it's very hard to do,' he told the BBC News website."
The two papers are:
"...Furthermore, because antisymmetry typically signals an environmentally triggered asymmetry, the phylogenetic transition from antisymmetry to directional asymmetry suggests that many cases of laterally fixed asymmetries evolved via genetic assimilation."
"...First, directional asymmetry, an evolutionary novelty, arose from nonheritable origins almost as often as from mutations, implying that genetic assimilation ('phenotype precedes genotype') is a common mode of evolution."
For recent posts on genetic assimilation see:
Featured books from the Science and Evolution Bookshop:
Wednesday, March 22, 2006
Re: Coming Soon: Evolution of the Lateral Line into the Ear
I haven't had much internet time for the last few days (and I'm likely to be busy until the weekend) but I thought I'ld post an 'update'.
Looking into the lateral line has certainly proved interesting - some possibilities have evaporated while others have appeared in their place - but my overall impression at the moment is that it may be more profitable (in terms of time invested) if I put this on hold and then come back to it later. I'll see how it goes!
technorati tags: lateral+line
Sunday, March 19, 2006
Coming Soon: Evolution of the Lateral Line into the Ear
On Monday I posted this Nature news item to the General Evolution News category:
"Why is our cochlea, the key organ of hearing, curled into a spiral? It has been often thought to be a space-saving measure. But researchers in the United States have shown that the spiral could be vital for increasing our ear's sensitivity to sound, particularly at low frequencies.
Daphne Manoussaki of Vanderbilt University in Nashville, Tennessee, and her colleagues believe that the snail-shell curve of the cochlea focuses sound waves at the spiral's outer edge, making it easier for vibration-sensitive cells to detect them1.
If the researchers are right, then the ear is more sophisticated than we thought. "
Not only is the article interesting in itself, but it brought to mind something I read sometime ago concerning evolution of the lateral line into the ear, and I thought it might make a good example of how such questions can be approached from the perspective of the proposed internal evolutionary mechanism.
I've spent quite a lot of time today trying to establish a 'baseline' from which to proceed, making sure I've got my facts right etc., but it may be that the notes will be very brief. It's a question of starting from the 'top' and then deciding how far down the hierarchy to go - I'll probably spend more time on creating the jpegs! Anyway, the post should give an insight and hopefully will be ready by Wednesday at the latest.
Saturday, March 18, 2006
Tom Stoppard, The Darwinian World, and The Declaration of Independence
Saturday is always a busy day and after breakfast (having decided to take a day or two off from writing about specific aspects of the proposed mechanism) I scanned the news headlines to see if there was anything about evolution in general that could be briefly commented upon in tonight's post.
"A matter of give and take" by Tom Stoppard in The Guardian (UK) caught my eye:
Tom Stoppard argues that free speech is not an inalienable human right
The idea that being human and having rights are equivalent - that rights are inherent - is unintelligible in a Darwinian world. It is easily and often overlooked that when Thomas Jefferson asserted that life, liberty and the pursuit of happiness were inalienable human rights, he did so on the ground that they had been endowed by God, our Creator.
That is how Jefferson deemed "these truths to be self evident". Yet, we do not find that insistence on human rights is the preserve of believers. Still less do we find the right of free expression being derived from God's endowment. Is the right of free expression self-evident?
That was all I had time to read so I printed a copy out and took it with me.
At lunchtime I read the whole article and was quite appalled. I felt that commenting at all would require commenting for hours (mainly about the role cultural conditioning plays in the forming of perceptions such as the world is "Darwinian") and so I decided to think of something else to write about.
On the way home, however, I felt curious about the context in which Jefferson had written "these truths to be self evident". As an Anglo-German living in the UK I have never read the Declaration of Independence, it begins:
When in the Course of human events, it becomes necessary for one people to dissolve the political bands which have connected them with another, and to assume among the powers of the earth, the separate and equal station to which the Laws of Nature and of Nature's God entitle them, a decent respect to the opinions of mankind requires that they should declare the causes which impel them to the separation.
We hold these truths to be self-evident, that all men are created equal, that they are endowed by their Creator with certain unalienable Rights, that among these are Life, Liberty and the pursuit of Happiness.
Words are only a reflection of the person who wrote them rather than a definition and in that sense, I would suggest, are not to be take too 'literally'. Furthermore, their precise sequences can be affected by anything from the 'mood of the moment' to the 'attitude of a lifetime'. Quite obviously Jefferson hadn't finished with the continuing importance he attributed to the "Laws of Nature" simply because he had finished the first paragraph and the words do not appear in the second!
However, the main point I wish to make, from the perspective of an internal evolutionary mechanism, is that life is individual and no excuse or justification is necessary for the existence of that life.
On the specific question of "Free Speech": when a person reacts negatively to the words of another it may be to the listener's ultimate benefit to ask themselves whether their response is innate or acquired - but also to ask the same question about the behaviour of the speaker!
Friday, March 17, 2006
Waddington's "The evolution of adaptations" gives a logical explanation of how ostrich callosities may have become hereditary but specifically refers only to those found "fore and aft" on the underside of the body.
On page 37 of "The Great Evolution Mystery" Gordon Rattray Taylor goes on to say:
Curiously, it [the ostrich] also has calluses on its ankles which are of no use to it, as it turns its foot sideways when sitting. They may, however, have been functional long ago when the ostrich had three toes and probably did not turn its feet over.
Yesterday's post, Re: The evolution of adaptations (Waddington) (2), describes how the callosities could have become hereditary from the perspective of the proposed internal evolutionary mechanism (the end result of the process being restoration of the 'localized area of equilibrium' to its initial state).
There is, of course, no "Law of Use and Disuse". But if, for example, consideration is given to the degeneration of the eye and loss of pigmentation in cavefish, then why have the ankle calluses of ostriches 'persisted' if they were "functional long ago"?
The answer is simple: When the ankle calluses became hereditary in the three-toed ostrich then contact between those areas and the ground would no longer have affected the 'localized area of equilibrium at the apex of the homeostatic hierarchy'.
During the transition from the three-toed to the two-toed ostrich the ankle calluses would still have had no affect upon the localized 'area of equilibrium'. Consequently, they are still there.
Eye degeneration and loss of pigmentation in cavefish, on the other hand, are examples of 'negative equilibrium' affecting the localized area and will be discussed in a future post.
This is the third of three posts on Waddington's "The evolution of adaptations". The other two are at:
The title link of all three posts goes to the Main Blog entry for Waddington's paper and this link goes to the paper itself.
Thursday, March 16, 2006
Preamble (for the benefit of new/future visitors): The concept of an internal evolutionary mechanism originates from the 'anomalies' referred to in " A Model of an Internal Evolutionary Mechanism and reflects a known single state.
There is a hesitation in extrapolating beyond this 'start condition', partially because the current mathematical model can only represent a single trajectory (see An Internal Evolutionary Mechanism and 'Direction in Evolution': Preliminary Notes) irrespective of how it is applied, but also because further development requires insight and research as much as 'logic'. For this reason the proposed mechanism will continue to be described as a 'localized area of equilibrium at the apex of an homeostatic hierarchy' (rather than, for example, any assignation along the lines of 'organs, tissues, and cells' to progressively lower levels within the hierarchy).
Today's extract from "The evolution of adaptations" is slightly shorter than yesterday's: the emphasis this time is on Waddington's description of the process whereby the callosities of ostriches become hereditary (rather than the intellectual strategy whereby the 'incredible' was reduced to the 'credible').
Having said that, however, I wonder if Waddington said "This may have seemed too long a train of argument to be very convincing" because of his own lingering doubts as much as any likely to arise in a reader.
After all, reducing the incredible to the credible was done within the framework of the 'modern view' of his day and its continuing dependency upon the discontinuity contained within setting up a "cybernetic developmental mechanism... rather like a gun set to go off when the trigger is pulled" and then subsequently waiting for the fortuitous arrival of a mutation sufficient to "pull the trigger". The human mind may be able to jump such gaps but perhaps the natural world is unable to.
...the ostrich squats down in such a way that the under surface of the body comes into contact with the ground at its two ends, fore and aft. In just these places a considerable callosity develops in the skin (figure 2), and Duerden  showed that these thickenings make their appearance in the embryo before hatching.
...It certainly seems very far-fetched to attempt to explain such phenomena without bringing in the fact that the environment might be expected to produce similar effects. Let us consider, therefore, what might happen to an ostrich in which the appropriate callosities were not hereditarily determined. Presumably its skin, like that of most other animals, would react directly to external pressure and rubbing by becoming thicker. Now the point which seems to have been overlooked in previous discussions of the matter is that this capacity to react must itself be dependent on genes. Since populations of animals are never quite uniform in any character, we must expect that the ostrich ancestors varied in their capacity to produce the most suitable callosities; and there could he effective natural selection for those which performed the most satisfactory exogenous adaptation. A race would evolve in which the stresses set up by squatting in a particular way would call forth the development of appropriate adaptive thickenings of the skin.
At this stage, the thickenings would still not be hereditary and independent of the pressure and rubbing; they would still be acquired characters in the conventional sense. We can find a hypothesis of how they might come to be hereditarily fixed if we turn to consider another aspect of the matter. The callosities are the results of developmental processes. Now, one of the main characteristics of animal development is that it tends to be canalized or buffered, so that the optimum end result is produced even if there are minor variations from the normal conditions while the process is going on . Natural selection, in fact, does not merely ensure that only those animals survive which have something near the optimum characteristics, but favours those genotypes which tend to produce such animals under any conditions. It gradually builds up efficient cybernetic mechanisms, to use a fashionable phrase. Thus we may expect to reach a stage in which our ostriches nearly always develop callosities of just the right size and position, even in those individuals which, to put it crudely, sit down very seldom or those which loll about the whole time.
Once such a cybernetic developmental mechanism has been built up, it will be rather like a gun set to go off when the trigger is pulled. The development of the callosities will proceed quite autonomously, once the process can be started. The initial stimulus, which may be a greater or lesser amount of external pressure, has become a relatively minor factor in the whole situation. It may then not be too difficult for a gene mutation to occur which will modify some other nearby region of the embryo in such a way that it takes over the function of the external pressure, interacting with the skin so as to 'pull the trigger' and set off the development of the callosities .
Before embarking upon a description of how callosities can become hereditary from the perspective of an internal evolutionary mechanism, it may be worth making the the following points:
1) Commentaries such as this one are not being offered as 'convincing arguments' in themselves. The primary purpose, in this instance for example, is not to argue that Waddington was somehow 'wrong' in his interpretation. The proposed mechanism is testable: these notes are more intended to show how natural phenomena can be looked at in a way that augments the argument for such testing to be done.
2) The ensuing references to "existing thresholds being exceeded" can not be more specific unless - for any organism - one or more instances of such an occurrence are already known. See Info wanted on two intriguing 'Lamarckian' experiments for possible examples of this.
3) Anyone who actually reads this post may reach the end and say "Thanks very much, but I'll stick with what I know!". There will be a third post in this mini-series (appearing either tomorrow or Saturday) addressing an interesting aspect which Waddington doesn't mention:
Curiously, it [the ostrich] also has calluses on its ankles which are of no use to it, as it turns its foot sideways when sitting [More]
As an additional 'enticement', commenting on the above will allow the proposed mechanism's relationship with the "Law of Use and Disuse" to be put into context.
How callosities may become hereditary
It is lunchtime and I am sitting in a Social Club busily scribbling away on the back of unwanted print-outs. From experience I know that if I continue this activity long enough today then the skin on the outside of my little finger will start to feel sore. Persevering for several days will eventually cause a callus with form.
The fact I consciously experience distress from the affected area indicates there will be a corresponding effect on the 'localized area of equilibrium at the apex of an homeostatic hierarchy' located within the 'older' (in evolutionary terms) structures of the brain.
Providing I do nothing further to aggravate the constant pressure on the outside of my little finger then formation of the callus will have three effects:
1) Tissue damage ceases at the site of the callus
2) Pain is no longer felt
3) The 'localized area of equilibrium', although 'offset' by the presence of the callus, is no longer affected by transient 'inputs' from the affected area - a state of equilibrium has been re-established.
If I persisted with the activity of writing for long enough within my own lifetime, and my (and other people's) descendants did so in theirs, then eventually the existing thresholds of the localized area of equilibrium would be exceded. Conceptually, this would trigger 'top-down' changes within the homeostatic hierarchy of the genome until the initial state of equilibrium has been restored (ie the 'offset' mentioned above would be gone). This would take 'n' generations, initially 'fast' but then tapering off, and it wouldn't matter if every pencil in the world disappeared once the process began. The 'size and shape' of the callus (as much as location and any other characteristic) would reflect the point at which equilibrium was restored relative to when no callus existed.
As usual I've finished far later than anticipated and any editing will have to wait until tomorrow (usually I see flaws the following day but move on regardless - after all the proposal is still 'under construction'!).
This is the second of three posts on Waddington's "The evolution of adaptations". The other two are at:
The title link of all three posts goes to the Main Blog entry for Waddington's paper and this link goes to the paper itself.