Like duh!

ANU Professor Dayal Wickramasinghe tells 666 presenter Ross Solly life could be everywhere in space.

Wish I could find the transcript

Evolution - The scientific method

I believe strongly in the development of evolutionary science, and I have new hypotheses that ought to be tested that don't contradict any experiments done, nor do they contradict the overall modern evolutionary synthesis. However, these hypotheses, if proven, may open up some arguments thought long ago settled.

The role of random mutations is well researched. These are well observed and are thought to be the basic unit of truly new, potentially beneficial adaptations.

DNA repair Is a process where damage to the DNA is fixed. This process is imperfect, however and failure in repairing mutations is a variable source of mutations. The process of DNA repair is blind to the function of the gene it is repairing. Thus, resulting mutations tend be in random places, and the build up of mutations on sections of DNA that don't change the function of the gene happen at a well defined rate. Thus, a process of feedback of information whether the gene is functioning properly, is the only way to account for genetic drift NOT occuring on important functional elements of the gene. Natural selection acting on whole organisms holding that gene is the only feedback commonly agreed on by evolutionary biologists to occur. However, my view is, that with a hierarchy of genes (ie. genes that control a bank of genes, that each control a set of basic genes that relate to a phenotype), there needs to be a hierarchy of feedback to ensure that the lower level genes are functioning. Ie. there needs to be a form of selection within an organism such that each basic gene can be selected or rejected based on its function independently of all other genes. The corollary being that lower level genes that are suppressed in some way by some higher level genetic action, can have its function ensured with the same process of feedback.

There are a number of mechanisms that could be at play to ensure functional integrity of genes, that are not natural selection between whole organisms. One of the mechanisms proposed, which is quite likely to be involved in some way is through the selective properties of sperm. In this mechanism, sperm act as selective proxies for the organism but specifically for genes lower down in the genetic hierarchy. Thus, every lower level gene affects the selective aspects of sperm, and that which gets to reproduce has fully functioning lower level genetics.

In this sense, this hypothesis is not concerned with the genetic variability due to the shuffling of phenotypes that follow the laws of Mendelian Inheritance, but only the functionality of the individual allele itself. This hypothesis takes it as a given that the spread of mendelian traits is the primary source of variability in phenotypes that are subject to selection in a standard Darwinian way. This hypothesis is concerned with: 1)How "improved" versions of alleles arise.
2) How stress triggers greater mutations.
3) How latent phenotypes not visible in a species can become common again.
4) How many "truly new" genes are involved in speciation, and how many genes are latent ones that are re-activated (or de-activated), or inserted via horizontal gene transfer, or are just a previously unobserved combination of mendelian and non-mendelian traits.

More Rants

There are clearly other biological hypotheses that have somehow graduated to the orthodoxy, such as Earthly abiogenesis. The hypothesis that non-life to life transition happened on Earth is a reasonably testable one, but a lot more mileage is given to experiments that assume early Earth origins (ie. that somehow Earthly origin is almost certainly the "truth"). However, I will concentrate on those biases against anything that remotely appears Lamarckian or like intelligent design (even if the intelligence is held within the DNA and/or the organism itself).

Now my thesis is that although the main feedback of information back to the DNA of how well it is doing is via the brute force of "natural selection" - that is a comparative between individuals with different DNA. However, my thesis is that there clearly is processes that are very much like selection that is also giving a feedback of how "fit" the DNA is. There are tens to hundreds of millions of sperm that are competing for an egg. The male is producing these and there may be a selection process from that side which strengthens those sperm with particular mutations and weakens others depending in part on the level and type of stress he is under. On the female side, the same thing is bound to be happening, with body conditions slowing down sperm with some particular mutations and letting through others depending on the level and type of stress she is under. As a final error correcting check, particular important sequences of genes are tested in the controlled conditions of the ova. The ova has been fully formed since before the mother-to-be was born. This is a rudimentary "archive" that checks on crucial DNA sequences to make sure there is no changes to those. Thus, a great deal of crucial environmental and/or competitive information is fed back to the DNA, as well as strict error correction on crucial segments during and even before conception. Thus the new organism will have had extensive pre-birth selection to give its genes the best chance of survival.

This might yet be uncontroversial - But it really depends on how sophisticated the stress to mutation-selection link is. To me it is plausible that there is a simulation engine powered by the subconscious mind that does intense calculations on how well any particular mutations may benefit particular constraints. Information can flow through the conscious mind, seeing certain genetic consequences, and the subconscious could translate it to stress information that would be selective for sperm proxies of the same genetic consequences. These would be really, really smart mutations - Much smarter than any genetic engineer could ever hope to become in following millenia.

The difference between the orthodox view and my view can be illustrated by a fashion paradigm. In the orthodox view, fashion designers make random changes to existing designs and force models to wear them. If they sell, they make more of the same. If they don't, the clothes get thrown in the bin and they don't make anymore of that crap.

In my view, what (successful) fashion designers do is that fashion designers make random changes to existing designs - show them to a test audience (of horny males, apparently :)) - changes that show some approval get kept. Process is repeated as many times as the exhausted sewing machinists and test models can cope with and then the surviving clothing is forced onto the model and onto the catwalk.

In my more sophisticated fashion design view, the machinists and models are given a break and all the experimentation with random changes happen on the computer (or a drawing board) and get shown to the test audience. By the time the design gets on the catwalk, the design looks "worked" and unlike the designs it may have been based on. To an untrained eye, it might still look like random changes, but those that *actually* put random changes straight on to the catwalk don't win the fashion show.

Additionally - to look at it another way the *winner* of the fashion show can gloat and make grandiose claims about his *creativity*, when in truth he just had a more sophisticated system of randomised changes with good feedback loop.

Marconomic Theory of Regressive Evolution

I will start with a generalised genetic disproof of inheritance of acquired characteristics from Wikipedia.Genetic disproof
There are many formulations of the genetic disproof, but all have roughly the same structure as the following:

Acquired traits do not affect an organism's genome.
Only the genome is passed to the offspring.
Therefore, acquired traits cannot be passed to the offspring.
While this proof may be logically valid, it suffers from the material fallacy of begging the question, since no one who believes in inheritance of acquired characters would believe both assumptions.


My theory throws these assumptions away and replaces them with this observation. The inheritance of acquired characteristics is not evident because the genome has embedded within it thousands of generations of experience as to what genetic traits are worthwile and those that aren't. In *general*, genetic mutations mimicking acquired traits do *NOT* make the organism any *fitter* to survive in nature.

Instead, the following rules of regressive evolution apply:

-Genetic mutations in offspring are a result of stresses on the parent(s).
-Mutations have a directed element that depends on the exact stress involved.
-The directed element is programmed into the genetic code via association between the stress which is acting as a trigger, and the mutation which has been "proven" to be appropriate to survive better under new conditions indicated by the stress.
-The strength of association between the trigger and the mutation is entirely dependent on the reliability of the trigger being an indication that the mutation is appropriate to the new "environment".
-Many of the mutations concerned are simply switching on or off complex functions that are permanently programmed in the genetic code whether they are active or not.
-Certain combination of stresses may create combinations of mutations without precedent in itself, but each mutation would have been "field tested" individually in distant or more recent history.

Examples that should be quite clear-cut:

Darkness stress: Species adapted to cave conditions or permanently underground (moles etc.) are uncannily blind whereas their closest relatives have full sight. The stress of being in darkness your whole life would cause a considerable proportion of your progeny to have genetic vision defects - all other things being equal.

Wetness/dryness stress: Kamerrers experiments on the midwife toad (Chapter 7 Panda's thumb) had some merit. Clearly, one must separate the selection pressure from the stress trigger to prove the point that mutations to switch back on genes that helped in water are not evident without the wetness stress. Experiments need to be formulated with this in mind. River-courses changing their path makes sudden changes in local environments.

Radiation stress: In Earth's history every single large scale event would have radiation associated with it. Volcanoes erupting, asteroid impacts, solar activity, and possible magnetic field fluctuations would all send rare radioactive elements in the atmosphere or increased radiation. Is it any wonder then that the most obvious, largest scale mutations are caused by radiation? It is a clear signal that radical mutations in any direction might cause some to survive better.

"Regressive evolution" as a term has been almost exclusively used in describing reduction of features, such as in the loss of eyesight and pigmentation in cave dwelling fish. In "Marconomic" terms, reduction in features is also the clearest example of it in nature. Switching off something that was there appears a backwards or downwards move, while the re-switching on of a previously inactive feature appears to be either a leap or not a truly new feature, depending on whether it had been observed before in related species. Philosophically speaking, backwards, downwards and leaps are artificial concepts based on thinking of evolution (falsely) as a ladder rather than the reality of it being a "bush". Switching on or off of features that are then passed on is adaptive either way. Thus I group losses and gains of such features in the same "regressive" boat.

I call it "regressive" evolution because the process almost always borrows tricks that have developed in the past with selection pressures optimising them. Switching them off saves resources when conditions dictate they are unnecessary. However, they are there for when they are required, and perhaps almost all of the evident "faster" evolutionary processes have borrowed perfectly working genetic tricks and combined them in new ways.

At first glance regressive evolution is not really evolution because it never introduces truly *new* changes. However there is such a large number of possible combinations of trigger-responsive genes that the number of species in the Earth is dwarfed by it. If there is a million genes that can be switched on or off depending on triggers, that makes two to the power of a million possible combinations. Virtually all of them will be truly new changes. Also triggers will almost always produce a spectrum of mutations - This is because the future cannot be predicted perfectly. Chance, probability and statistics is a big part of the process. Truly random mutations, however are almost certainly an evolutionary dead-end.

So I have said that in *general*, genetic mutations mimicking acquired traits do *NOT* make the organism any *fitter* to survive in nature. However, this begs the question: Is there any *specific* genetic mutations that do? (Mimick acquired traits that triggered the mutation)?

The trait/mutation would have to fit the following conditions:
A) The organism must be in a state of life or death stress or reproduction-challenging stress(1)
B) The "situation" must be very analogous to situations repeated in the genealogical history (2).
C) The mutation must clearly help progeny in analogous stressful situations more than just being shown/trained/helped by the parent(s) etc. (3)
D) The disadvantages of the mutation must be clearly outweighed by the advantages given assumed environmental constraints. (Needs a clear cost/benefit advantage)

(1) It is not enough, for instance, that a giraffe stretches their neck reaching for higher food. For a trigger situation, the giraffe must see other giraffes dying of starvation, be short in food itself, and endure the frustration of seeing lots of leaves just out of reach. (Using a well known Lamarckian example) If it isn't a life or death situation, the mutation will be both unecessary and resource-depleting.

(2)The "knowledge" associated with the trigger must be on firm statistical ground. The trigger will never be something only associated with proximal individual adaptation. For instance one 1930's experiment devised to investigate inheritance would chop of an insect's antenna that generally grows back. Any number of generations "experience" would not offset the natural experience of the insect, which is - that a more ideal regrowth of an antenna is unnecessary for survivability and reproduction in any conceivable natural environment. Even if it was - chopping off an antenna would not be an indicative trigger.

(3) It is tempting with certain features, to assume that if strength in one arm is important to survivability, and a person strengthens that arm for a greater part of their life to suit their job, and that their children are likely to have the same constraints - that a genetic mutation that would strengthen that arm without as much training would have evolutionary merit. However, if the feature is being passed on to the child by training from the parents, and very few are dying due the the arm being too weak, a mutation may be less reliable than just letting the parents train their children specifically.

A Rundown of evidence that supports my theories:

1) Experiments show that general mutation rates increase as a result of stress.
2) Humans and bacteria have some parts of their genome that are extremely similar. Even though these same parts are quite resistant to random mutations (ie. random mutations do no noticeable change to the organism). As with most parts of the genome, the specific functions of these segments are unknown.
3) Natural selection needs mutations to select from. Stressful situations lend themselves to particular mutations. This article lays out a clear example of adaptive mutation. Because almost no research is looking for similar adaptive mutations, it is unclear whether this is the exception or the rule.
4) My theories do NOT rule out random aspects to the process. Genes that *Are* under constant selective pressure will have (seemingly random) mutations and will use natural selection as a process of refinement, quality control and mutations that don't affect the purpose of the gene will build up in that gene over time -*at well researched rates*. Selective pressure is the error-correcting mechanism in this case and certain critical sequences can stay the same for Billions of years by this mechanism. This fits in perfectly well with my theories.
5) The apparent extension of this randomness into virtually all genes fits the data quite nicely. However, this should not rule out that the apparent randomness overall, is due to the randomness of the factors that cause mutation triggers. The orthodoxy is that the apparent randomness rules out environmental feedback causality of most of the overall apparent mutations. As pointed out in (3) there is some clear counter-examples to the orthodoxy.

Arguments for modern specific experiments for Lamarckism

I have been reading The Panda's Thumb and there is a nice chapter devoted to the discussion of Lamarckism. Essentially the tenets of "Lamarckism" is that evolution can be "directed" by environmental factors, rather than by undirected genetic variation being winnowed out by death or lower reproduction rates of fellow individuals of the species allowing the remaining individuals to pass on genes appropriate to the environmental factors. Lamarckism has been rejected by biologists because "Darwinism" explains all facets of evolution satisfactorily, and no direct evidence of Lamarckism has been discovered, as well as the fact that particular examples (giraffe necks etc.) oft quoted have been discredited as being both explainable by darwinism and having no measurable direct evidence of directed genetic change.

A new approach would be to look at it from a completely different angle as follows. If Lamarckism is a force in evolution, what are the best genetic strategies to follow given a pre-reproductive youth to experiment on what genes are useful and which not. The issue to me is that genes would have to predict what future environments will require. Genetic variation would hedge its bets on an environmental change being a temporary or permanent one. I would suggest that modern controlled experiments on a range of different animals over a large number of generations would demonstrate it. Essentially, almost no experiments have been done since the 1920's and 1930's. With a greater understanding of the complex role of RNA, more nuanced experiments, I believe would find a subtle but pervasive pathway for some direct/accelerated forms of evolution.

Neither the rat/maze learning experiments and antenna/amputation/regrowth experiments have natural environmental analogies, making them less explanatory than they appear. Direct adaptation would only happen where similar changes in environment had happened before in the distant ancestral history of the animal/plant in question. After all, the specific Lamarckian adaptation itself would have to evolve to suit probable dramatic shifts in environment (ie. selection pressures on species that had no Lamarckian adaptation vs species that did)

One particular experiment would be subjecting specimens to permanent darkness. It is a well known evolutionary theme that vision in a large range of beasts becomes impaired when adapted to permanent darkness. It also has reasonably common natural analogy where animals adapted to light have close relatives adapted to dark with common ancestry. Adaptation to permanently, cold, wet, hot or dry are similarly common natural events that lab experiments could weed out direct vs undirected variation.

Delusion XVI - Chapter 5 - let the atheist scientist attack

I had an idea to extend on "Adaptive? Aye!" and attack Dawkins *With the assumption that the conclusions of the previous four chapters were correct* (in fitting in with my axiomatic abstractions) , However this Skeptic of Dawkins has done most of the work for me.
Average effects became selfish genes and individuals became lumbering robots controlled by their genes. Group selection became a pariah concept, taught only as an example of how not to think. As one eminent evolutionist advised a student in the 1980s, “There are three ideas that you do not invoke in biology: Lamarkism, the phlogistron theory, and group selection.”

I invoke two of those three (Lamarckism and group theory) and I add "panspermia" as an alternative third, that have been "ruled" false, yet I am convinced that these three "facts" will be reversed within our lifetime by good science.

Scientific Dogmatism
In retrospect, it is hard to fathom the zeal with which evolutionists such as Williams and Dawkins rejected group selection and developed a view of evolution as based entirely on self-interest

That chapter five is based on Atheist Dogma, to me is a tautology. An atheist skeptical scientist appears to back me up. David Sloan Wilson basically covers all my objections of chapter 5, that Dawkins is choosing to believe the theory that makes religion look all the more pointless.

I can't help but include his conclusion:
On Scientific Open-Mindedness
Toward the end of The God Delusion, Dawkins waxes poetic about the open-mindedness of science compared to the closed-mindedness of religion. He describes the heart-warming example of a scientist who changed his long-held beliefs on the basis of a single lecture, rushing up to his former opponent in front of everyone and declaring “Sir! I have been wrong all these years!”

This inspiring example represents one end of the scientific bell curve when it comes to open-mindedness. At the other end are people such as Louis Agassiz, one of the greatest biologists of Darwin’s day, who for all his brilliance and learning never accepted the theory of evolution. Time will tell where Dawkins sits on the bell curve of open-mindedness concerning group selection in general and religion in particular. At the moment, he is just another angry atheist, trading on his reputation as an evolutionist and spokesperson for science to vent his personal opinions about religion.

It is time now for us to roll up our sleeves and get to work on understanding one of the most important and enigmatic aspects of the human condition.

Obviously, I believe that Dawkins is close-minded about this, and Atheism as an ideology will be as close-minded as any other "religion" for the foreseeable future, with such spokespersons as Dawkins.

The Polar Bear "species" is 100% safe from global warming

Environmental "scientists", I believe have been guilty of Species Inflation with regards to polar bears. One of the things that evolutionary and genetic science has given us is a "tight" definition of a species. Ignoring the look, habitat and lifestyle and just concentrating on the genetics, polar bears are a sub-species of the brown bear. Focusing on the plight of the white bears is just racism.

Historical Sciences Bah...

I am not really a big fan of the historical sciences. To me it makes a mockery of the word science(*). Scientific method is about repeatable experiments, and everybody knows that... "His-tory neever repeats...". Also, one can always quip back to some asserted historical fact - "Were you there?" you know to "observe" it. Indirect observation, irrepeatable conditions = always conjecture. This especially irks me when experts in their field go to extreme lengths and expense to prove for example A) that Jesus performed miracles or
B) that a particular fossil is the common ancestor of apes and humans.

To me these factoids are primarily used to enforce one's theological convictions, and are therefore pretty useless scientifically.

Even historical ice cores for temperature & atmosphere content statistics have gone as far as is scientifically useful. Todays conditions and issues are so radically different to historical ones, that it cannot help policy decisions today, and are therefore again only useful in promoting ones views (perhaps at taxpayers' expense).

(*) - To tell you the truth, I probably just have a problem with the "SPIN" placed on historical sciences rather than the historical science itself.

Dissecting articles from Realclimate.org

WSJ Editorial Board: Head Still Buried in the Sand
Filed under: Climate Science RC Forum— group @ 8:38 am
While the rest of the world has basically accepted the conclusion of the latest IPCC report, one small village still holds out against the tide - the Wall Street Journal editorial board. This contrasts sharply with the news section of the paper which is actually pretty good. They had a front-page piece on business responses to global warming issues which not only pointed out that business was taking an interest in carbon reduction, but the article more or less took as a given that the problem was real. However, as we have pointed out before, the editorial pages operate in a universe all their own.

I will start with their latest headline piece - It is very typical anyhow. As far as the title goes, using a metaphor is a form of "proof by ridicule". What exactly they are trying to prove is not obvious to start with, but the means they are using is attacking an opinion piece. To falsify a scientific statement you must use science, to falsify an opinion you must use ridicule. Fairly obvious, but they are not really showing their hand.

The first sentence uses the terms "village" and "Tide". I am not sure if this is subliminally pushing the "sea is rising" fear triggers, but is the tide public opinion? Public opinion of what? The tide is of pro-environmentalism and the village is of dissenting opinions published in news & magazines. Almost all magazines (including "the Economist") have stopped publishing dissenting views (whether they be scientists or whatever). I am not really sure why that is, but for instance, the Economist has not recently written anything at all from Bjorn Lomborg, while a couple of years ago, they backed him up in almost everything he said.

The third sentence mentions business responses and interest, and the taking as a given that the PROBLEM is REAL (by the front page article). The science demonstrates beyond reasonable doubt that there is global warming and that humans are the predominant factor. That it is a "problem" is a much less scientifically tested assertion. Proving that there is global warming and that it is caused by humans does not prove that there is a problem in itself. Also, there is the assertion that it is the most significant environmental problem. This assumes a prioritised list, but prioritised lists have been rejected as presumptious.

The fourth sentence is again criticising the opinion piece, and again ridiculing it. I have found this type of tactic in operation with groups of evangelical christians. It was exceedingly effective when used in groups of majority christians and a minority of uncommitted youths. They would ridicule (say) evolution, and attack the inconsistencies of darwinism and any proven errors any Darwinist has ever made. It is difficult for an uncommitted person to resist this kind of peer pressure. I think this is what is happening in Realclimate. There are a majority of readers which are "converted" and a minority of uncommitted and recalcitrant, which is a perfect environment for winning over the uncommitted.

Thermodynamics - It's more than just a good idea. It's the LAW

I do think that the 2nd law of thermodynamics is one of the fundamental rules of the universe. In some ways it defines the direction of time. Other fundamental rules (such as the first law) and laws of relativity and gravity distort perceptions and models of time. In some ways I don't really want to get into the mathematics of it all as to whether it excludes a continually existing universe. I can either take the cosmologists word for it that they have done their science right and accept what they come up with as a consensus, or I can just latch on to whatever dissenting view there is and claim the question as an unknowable.

"Darwinism" as a staircase

The front cover of the economist christmas edition shows the classical subliminal message that human evolution is about progress up the ladder (staircase in this case). Although the actual article does rail against the popular concept of "survival of the fittest" because it completely mis-states the reality; it does mention such things as "progress", "great leap forward" as scientific concepts of what was happening at various stages. Genetic palaentology has been able to put accurate dates on common ancestry, which is really illuminating. Great science is happening, but darwinism as a popular ideology doesn't require it. To remain popular, Darwinism must still place humans on a pedestal above other living things. This is to replace the "specialness" that is given to humans in various religions. Because, in general, Darwinists profess to be non-religious, why should they care what happens to the human race if we are not special or superior to animals?