Saturday, March 14, 2015

Letting Go of Abiogenesis

In an earlier post in regards to standard evolutionary synthesis, my point was that simple "natural selection" on "random" mutations fails for the very Darwinian reasons the idea originated from. If it ever was the primary mechanism, it would have died out quite quickly from obviously superior mechanisms (that are, nevertheless adaptive in the same intuitive sense for reproductive success). At least, that is my conclusion and thesis.

Looking at a particular *new* *beneficial* mutation that one time or another has to happen on a path to some species to another more adapted to a particular environment, the probablistic difficulties are similar in scope to what is envisaged in abiogenesis, but of course, having working and sophisticated superior mechanisms already in play is different from something where you really only have the laws of physics, chemistry and probability as envisaged with abiogenesis.

All efforts to demonstrate in principle either backwards from the simplest life we know, or forward from the most complex non-living carbon based systems we can imagine, have come up with a blank. It reminded me of the difficulties and paradoxes with Euclid's fifth Axiom, and also the paradox with measurements of the speed of light being constant at different relative speeds. Most who research abiogenesis in some way or another don't perceive the paradox so much as it being difficult to conceive and not having evidence to lead you in any way or another to point in the right direction.

My idea was to, like mathematicians in their time, presuming Euclids fifth axiom false, or Einstein in his time, presuming the speed of light to be constant at all relative velocities. If one presumes abiogenesis as currently framed to be not just difficult, but actually impossible, where does that leave us with naturalistic possibilities with the origin of life?

My idea was to make this a bold falsifiable theory, and hope that some evidence would actually bear on it to rule it out or not. Certainly it makes perfect sense to me, but I want to give all support and aid anyone who thinks it can be proven wrong by some experiment or new observation.

My alternative to a process of abiogenesis to go from no life to chemical life, is instead that chemical life is designed (in an evolutionary process of design) by a life form which is not directly chemical based. I was thinking along the lines of Hoyle's dust cloud life as something at a similar place in idea space. My other thought was that the proximal antecedent to chemical life would use its own life cycle as a kind of template for the first independent living cell, which would have to be something like an amoeba.

When I first saw the image of Hartley 103P with these abiogenesis ideas in my head, I felt that comets were the only real candidate for life's proximal antecedent. Over spans of thousands to millions of years, they use the interplanetary superhighway to move from orbit to orbit expending very little relative fuel. To reproduce, they expend a great deal of energy speeding up their spin in a controlled way, stretching into a bilobed shape then continuing the spin up and stretch until it is two almost independent bodies tethered by a long skinny neck, which tidal alignment would easily sever "the umbilical cord" and the two separate comets would go their separate ways.

In light of this, for most of their lifespan, comets would be completely "dormant" and essentially invisible. Thus dark "asteroids" like Bennu, which is likely to be visited soon enough should have almost all the same features as comets, bar the outgassing. The distinction between live/dormant comets and 
dead asteroids would come down to colour - the lighter they are, the less likely they are to be just dormant, and features dominated by impacts rather than cometary flaking/stretching/outgassing would be a "dead" giveaway.

Anything opposite to this, I would feel would easily falsify my hypothesis. It being based on assuming abiogenesis as currently framed impossible, and comets being the proximal biological precedent. The former being broadly "M life theory" and the latter "living comet theory"

Quite frankly, I'd be very satisfied if they were falsified - my investment in the theories is based on an unshakeable hunch that they are right. I want to find evidence that they are wrong - please help me.

Sunday, March 08, 2015

The collisional Problem (reblogged from Scute1133)

original post


“The Collisional Problem”. I might have dreamt that up as an apt subtitle for this post because by the time we’re done it will surely be merited but, too bad, I was beaten to it. Those words were already taken as the subtitle for a poster accompanying a talk on 67P’s status as a contact binary. The venue was the American Geophysical Union (AGU) Fall Meeting in December 2014 and the verdict on that binary status remains equivocal.

The abstract for the presentation was entitled,”The Nucleus of Comet 67P/Churyumov-Gerasimenko : a New Case of Contact Binary?”

It acknowledged that:

“A contact-binary among the Jupiter family comets (JFC) such as 67P would have profound implications since it must be primordial and the comet must have survived a possible history of collisions in the Kuiper belt. The present cumulative distribution function of size of nuclei of JFC comets indeed suggests a collisionally-relaxed population.”

In other words, there is countervailing evidence that militates against the existence of contact binaries in such a “collisionaly relaxed” population.

The collisional problem is, however, just the first of many for the CB theorists. They might be able to attempt an explanation of the rotation plane head-tip and fractures but not without jumping through flaming hoops in the process. They seem up to the task though. The AGU abstract considered the “unlikely…scenario of a re-accumulated body following a catastrophic collision” (because it really ought to have been blown to smithereens by now), as if it was a last resort to explain the two-lobed shape as a contact binary.

True to say, everything should be considered. Asymmetrical erosion (carving out the lobes via lopsided outgassing) was given a fair hearing too. But it seems the notion of ditching both theories altogether and contemplating stretch theory was just one step too far. 

At least one of those authors presented again two weeks later, at the American Astronomical Society’s 225th meeting (AAS 225, 4th to 8th January 2015), still referring to 67P as a contact binary or possibly a single, eroded body. Again, the phrase “a new case of contact binary?” was used, along with the poster, still reminding us of the collisional problem.

But the answer to the collisional problem was on the poster itself! It had a picture of the comet, looking straight down the z axis of rotation. The visible perimeter, the horizon, was therefore the xy rotation plane and the lower-right horizon was where the fractures happen to straddle the neck at 90 degrees. Furthermore, the uppermost tipping of the head kisses that horizon line too, right above the fractures.

That poster was what made me twig the relationship between rotation plane, spin-up, head tip and fractures that lead to this twinned pair of posts. So the answer to the collisional problem is what it was telling us all along- that 67P can’t be a contact binary. But you had to let go of CB theory fully, if only momentarily so, in order to see the hallmarks of stretch theory depicted on that poster. They are crying out at us: rotation plane, head-tip, fractures.

Here’s a tweet of “the collisional problem” poster:

Not much AAS 225 or AGU 14 material is available so we had to rely on tweets. I believe that at least two tweeters quoted here were present at the talks and the third, possibly so, or an astronomer with a live feed of some sort. I can’t be certain of this but they all seemed informed and genuine. 

Respondents to the above tweet and elsewhere on the #AGU14 hashtag, some from respected institutions, were happy to support CB theory. One suggested tidal friction leading to tidal locking (of head and body) and then settling against each other. Another supported the asymmetrical erosion tack but no one considered stretching. 

Incidentally, I can’t imagine a secondary with one side as flat as that shown in the photo below, offering that side up to the primary in an attempt to lock tidally. It would be inherently unstable. If it ever locked at all it would only be stable if it was the other way round with the topmost ‘crater’ facing into the neck. The reason it’s stable in stretch theory is because it always had a supporting neck to attenuate excessive tipping via compressive resistance to any downward vector on any side. This would even have been the case when it was ‘weightless’ during the stretch because the ‘locking’ referred to above is in two of the three rotational axes of the head, not its translational stretch. There are signs this compressive resistance did indeed happen because the head tip only went so far. Here’s the photo:

2015/01/img_22231.jpgPhoto from Part 10. Blue dots: xy rotation plane; yellow dots: ends of one fracture among several. 

Of course, this remarkably flat underside of the head can now be seen for what it is. It’s simply the extension of the now well-documented cliff, reemerging on the other side of the neck. This was the first photo to come out that showed it, proving the head lobe has a flat underside all the way across and overhangs the neck evenly on both sides. The entire plane seats itself back down neatly all round the currently visible portion of the comet body and will doubtless prove to do so on the dark side when it comes into view.

At another AAS 225 presentation, 67P was presented as a contact binary, plain and simple. The presenter pointed out that while several other comets had rocks joined end-to-end, this one had one on top of the other so it looked like a sphinx. That’s actually a far from fatuous distinction, though I’m not so sure anyone was aware of the fact. It should immediately point to the reason the head is tipped up at the back and lead on to the underlying mechanism at play: spin-up, leading to head-tip, stretch and transverse fractures. The head was thrown forward during spin-up due to the very fact that it’s “on top” and not at the axis extremity. But this fact becomes clear only if the rotation plane is considered. 

So, yes it does look like a sphinx but the contact binary assumption made on the way to that conclusion is troubling. The “on top” reference was unwittingly portentous but it became just an interesting observation in the absence of any willingness to loosen the grip on CB theory. Here are the relevant tweets:

The presenter went on to say that the fractures in the neck were due to the head rocking against the neck. That’s true up to a point. It’s due to the head tipping forward during the stretch, among other things, but “rocking against” (the tweeter’s words) suggests random movement with no known cause. Here’s the tweet:

As if this succession of respected presentations wasn’t enough to leave stretch theory buried for good another American Geophysical Union presentation, on December 18th 2015, managed to take all the evidence as presented in Part 10, which proves the comet stretched and use it, in error, to prove the exact opposite: that 67P’s shape resulted from the head lobe crashing in from the opposite direction. A sure case of a contact binary. Here’s an article from Wired magazine that reported on that presentation:

The reasoning went that, seeing as the strata in the head lobe and the body lobe don’t align, they can’t be related and so they must be two different bodies that drifted together. But the only reason they don’t align is the simple fact that the head has tipped up, taking them out of alignment. The Wired article explained that using new images taken with Rosetta’s OSIRIS camera, the presenter and his colleagues found “terrace-like layers” on the comet’s body and that:

“The layering aligns perfectly with parallel lines seen on the opposite side of the body, suggesting that these layers extend through the body as part of its internal structure. Although the head also has layers, they don’t align with those in the body, which implies that the two lobes were once two separate pieces. If the head and body were made from one piece, the layers should extend through both lobes in the same direction.”

This line of thinking presupposes that the only alternative to contact binary theory is asymmetrical erosion gouging a scoop out of a single rock. The only way the presenter could envisage the strata lining up through both lobes was in the scenario where a single body started out with its strata intact all the way across and then this scoop was removed, leaving the two separate lobes but with their strata still in alignment. 

That assumption is what steered the presenter away from the most obvious solution- that the head had tipped up, taking the strata out of alignment. If it was tipped back down by 30-40 degrees and seated onto the body, the strata lines would align perfectly, as demonstrated in part 6 of this series.

But it was the head-tip itself that led him to believe that that strata had always been out of alignment so this crucial piece of evidence that so strongly points to stretch theory was used unwittingly and in error to ‘prove’ instead that contact binary theory is correct.

That is a perfect example of the adherence to a cherished theory blocking out even the very thought processes that might lead to the correct theory- a case of fitting new data to an old way of thinking, rather than letting new information speak for itself.

It is also of note that this hypothesing around the finer points of CB theory is based on the highest resolution photos from the OSIRIS camera on the Rosetta orbiter. Just a few scientists are privy to this data at the time of writing (including those with the collisional problem) and it was my honest opinion that they could not help but alight on stretch theory with the abundance of evidence before them, much of it still to come in the next few parts of this series. 

However, the Wired article went still further:

“The neck of the comet also shows signs of a collision between the head and the body. The region is covered in big fractures, [the ones straddling the xy rotation plane in the photo above] which would have been created by shockwaves that blasted through the comet during a crash. Some of the fractures are also misaligned, suggesting that they belonged to what were separate, smaller chunks that were floating around when the head merged with the body.”

I have never seen a compressive force cause fractures in a concave surface without it resulting in an explosive shearing event. There’s simply nowhere else for the material to go. Witness compression-testing of concrete pillars that aren’t even concave. They explode dramatically. If further compression of the comet’s neck material is invoked to counter that claim, it is self-contradictory because if it can compress still further it won’t fracture. Indeed, with a porosity of 74%, the neck would have plenty of give in compression and at most it would simply bulge out in folds. But it would not fracture under compression unless it sheared violently as well. 

The fractures have clearly resulted from tensile, flexion and torsional forces none of which are compressive (except where flexion compresses the opposite side of the neck). 

Incidentally, the mention that the fractures are ‘misaligned’ is interesting. Their average direction is distinctly at right angles to the rotation plane and in successive parallel lines. Yes, they do make noticeable excursions from that simple large-scale picture, presumably due to structural anomalies, but the overall impression is as presented in the photo above and the others in Part 10 (reproduced below). 

So, according to this second AGU presentation, as well as the head rocking against the neck (on the sphinx), it had first of all collided with the neck, which was apparently ready-formed, protruding into empty space and pointing in exactly the right direction to make the catch. Once captured, the head ended up perfectly centred with its flat plane conveniently facing downwards, allowing it to overhanging evenly all the way round the neck. That’s quite an impressive claim, provoking at least four tough questions.

Moreover, even if the idea of the colliding head causing the fractures appeared to have some merit at first glance, it wouldn’t explain why those fractures are clustered in parallel lines, at one end of the comet, exactly straddling the rotation plane, at 90 degrees to it, sitting right under the most tipped-up part of the head, and found nowhere else on the neck.

That’s six more really tough questions, ten in total, for the CB adherents to answer regarding the collision of head and body- and that’s the real collisonal problem here, the one that truly merits the subtitle.

The simple answer is that this is where the neck stretched the most and the head tipped forward. Stretch theory would not only answer those 10 questions with ease, it would also predict all ten outcomes as being highly likely.

If they did somehow manage to jump through all ten hoops, the CB theorists would then have to go on to explain why the plan-view matches between head and body were irrelevant- along with their corroborating 3D matches (Parts 1-5). Then explain away the ridges that straddle head and body, followed by the matching strata layers (Part 6). After that, the 30-metre uplifted ‘gull wings’ and slurry piles arising, apparently, from gentle sublimation (Part 7). Then the dykes (Part 8), and the missing slabs (Part 9) -of which there are several more to come- and at least three more as yet unpublished pieces of compelling evidence. That’s eleven more hoops, twenty-one in total to date and counting.

Sorry, twenty-two, I forgot the the original “collisional problem”.

In conclusion, stretch theory answers a multitude of questions that contact binary theory cannot hope to address. Yet on January 8th 2015, the day that AAS 225 closed for business, and astronomers and reporters tweeted views of Seattle en route to the airport, stretch theory had yet to see the light of day.

Copyright ESA/Rosetta/NAVCAM – CC BY-SA IGO 3.0
Here are the other two photos from part 10:



Tuesday, March 03, 2015

What is wrong with standard evolutionary synthesis

With this explanation, I will use terms that may normally be associated with informatics. This is strictly in use for shorthand in the same way that "running the program" is expressing the genes that are associated with DNA that may or may not have mutated. It should be in no way taken to mean that it is scientifically accepted to use the arguments made of a Turing machine or computer science to come to conclusions in regards to Dna mechanisms. 
Also, I am not big on citations. I may mention people like Popper, Wickramasinge, Lennox, etc. but not based on their authority on any subject or another. My thoughts are to be considered based on first principles, and perhaps more abstract like in a mathematical argument rather than a debate scored by a selected audience.

Looking at the synthesis in historical terms, it has evolved from Darwinism, where the main thrust is the origin of species. Life on earth, when exposed to a different environment will adapt to that environment over generations. This was documented and well observed in the Galapagos. Extrapolating from the changes in observed Galapagos species from mainland ones, to the length of time of the age of the earth, it is quite logical to extend that process to all known species. Naively, the process was seen to extrapolate back past the Last common ancestor, and Darwinism included abiogenesis in a kind of continuum from no life to the variety we see today. Now, in maths as in science, interpolation is always a safer bet than extrapolation, thus two species which are closely related in time, genetics and space can confidently have intermediates placed in there, and have a rough idea of smaller changes over time leading from one to another. Extrapolation beyond the last common ancestor is a completely different kettle of fish, because we have no evidence to go on at all, but at any rate, in a philosophical sense, belief in evolution is highly correlated to a belief in abiogenesis.
This leads on to the hypothesis of "how" adaptation happens. In the case where a beneficial mutation reflects a particular environmental "selection", I will use the shortcut that the environment "programs" that particular mutation. As said in the first paragraph, this is just a shortcut, in no way am I ascribing informatics to the process. In this sense it just means that selective pressures are colluding to give differential advantage to individuals and/or groups and/or populations that end up with that mutation. For the individual that first gets this mutation, this is like winning at the roulette wheel. Blind watchmaker analogies and the use of the word random imply that there need not, and probably is not any direct or indirect, partial or even trace causal interaction between the environment and the beneficial mutation. It is like the roulette wheels are assumed to be perfectly balanced, the programming is strictly done, and only done by selective pressures, which involves more successful reproduction and survival with than without.
Clearly the "goal" of a beneficial mutation is one which better enables survival in a (perhaps changed) environment, and of course the environment will have the final say, but Darwinially speaking, a more (even trivially more) efficient programming technique than that envisaged, by a "blind watchmaker" will *always* win over the completely causally unconnected technique. Thus just as "fitter" organisms will win over the less fit even at the cost of extinctions of some of the less fit species, so too fitter "programming systems" will win over "blind watchmaker" programming systems.

This is perhaps like saying that roulette wheels are trivially non-level, but professional gamblers that measure the level in secret, and know exactly how to win will consistently end up in front while everybody else will lose to the house.

The "environment" is replete with symbiotic organisms that are both part of the environment, react to environmental cues, cause trivially non-random mutations in other organisms (eg through causing stress, horizontal gene transfer, activity of viruses, transport of mutagens, etc.) and thus can allow organisms to "beat the house" of the blind watchmaker. Species that do not or cannot have these "programmer helpers" will have much less chance to thrive under new environmental stresses. 

This is the crux of my argument that natural selection on random mutations *cannot* explain adaptation that is as efficient as observed in, for example resistance to pesticides, because more efficient adaptations win against naive randomness and brute force selection any day.