Science

My subjective take on issues in and around science. Profiles of interesting scientists, etc. Also, juicy videos of nature, physics, and chemistry, etc.

Actual Science

The scientific model is a glorious invention for exploring our universe. The simple rules, if honestly applied, are self correcting, grounding us always in a testable connection to truth. In establishing any fact, it unburdens us of ignorance about that fact not just now, but forever. It moves our piece that many squares forward. Best of all, new and meaningful questions arise which can be explored from that knowledge. Science fractures the unknown, then explores all the cracks and finds unforeseen goodies everywhere: Telescopes, antibiotics, vaccines, better food.  You could say “Like magic!” except, you know…it isn’t. As science got rolling, and gained momentum it also gained the respect that comes from undeniable results.

Science is earthy and practical and performed by people with an improbable and hard to explain love for things like soil or beetles or cancer cells. To the extent that any of us not actively working in science actually “Fucking love science” it’s probably due to the purity, passion and goodness of these nerds. They are the real and lovable thing. (my later complaints about “sciencey culture” are not about these guys) I don’t mean they are all adorable geeks out of central casting, but they have the temperament and interest to patiently keep close company with small simple details of experiments as they change across time, recording them accurately, and leaving a trail that could be followed later. They always understand what the experiment COULD mean in this outcome or that one but they play no favorites, knowing that to do so IS NOT SCIENCE. Therefore there is a core of disciplined virtue within every well conducted experiment. Every honest recording of a disappointing outcome is a public service, promoting the health and strength of the community. There’s no big reward for that, it’s just doing the job as it must be done. How many jobs utterly depend upon carefully documenting and sharing the truth?  Continue reading

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Scientists taught white mice to fear the smell of cherry blossoms.

(“So Bob, what line of work are you in?” “I frighten mice, like my Father and Grandfather before me..”)

The offspring of these frightened mice were never subjected to this cherry blossom trauma but mysteriously, they also feared the smell. More amazing still, the grandchild generation of the original trauma mice, also never subjected to the treatment, reacted with fear.

This is the classic cited example of Epigenetics or Soft Inheritance. The traumatic experience memory is passed along not by DNA, but by methylation changes on the DNA. It’s the DNA equivalent of working memory between generations.

In the old synthetic theory, without soft inheritance:

Two squirrels are living at the same time, in the way, way back when. Along comes a saber-tooth cat. Both squirrels run but the faster one survives and the slower one doesn’t.
Ergo->Faster squirrel genes move one step forward and thanks for playing, slower squirrel genes!

And now, with epigenetics:

Same time, way, way back when. Two squirrels again, different scenario. One squirrel has a close encounter with the saber-tooth cat and gets away, badly shaken but alive. The other squirrel was obliviously examining his nuts in a tree nearby. He never saw the cat, and he is unaffected. Squirrel number 1 has babies and they are born with a fear of cats or at least an extra sensitivity to “something moved!” Squirrel number 1 has enhanced his reproductive status by communicating a mission-critical message to the next generation and the one after. They are literally BORN with more “street smarts” than squirrel number 2’s offspring.

What does it mean if a creature inherits some of the important EXPERIENCES of at least two generations of its ancestors and possibly more? This breakthrough model is fascinating because it describes a form of parental teaching of life lessons to the young in species that can’t archive data or tell stories. Instead, they attach a little chemical post-it note to their genes saying “Beware of Cat”.

If asked “how could the genes know “Cat”? I’d answer “The same way they knew about cherry blossoms.” It’s staggering to think of the sophisticated mechanisms involved and questions rise like mountains in the near distance. Actually, it’s one question, repeated.

1. Something terrifying happens and a sort of snapshot of the event is taken within the organism. How?
2. Which captures details of the experience. How?
3. Ranking some as meaningful. How?
4. And retaining them. How?
5. Ultimately initiating a process that hands this information off to the sex cells for the next generation. How?
6. This new generation “knows” this life lesson as if they’d lived it themselves. But How?

We have now reached the “Talking out of my ass” section.

The thing that gives me shivers (of excitement) is the list of things that must take place for this to work.

  • There’s got to be a threshold of some kind. How intense does the experience need to be to “make the cut”?
  • There must be a mechanism that takes these “Must know” memories out from all the other memories and decides to engrave them on gametes.
  • There must be some crazy-ass coding that allows methylation changes on DNA to communicate details like the smell of cherry blossoms. That would be a highly specific molecule banging into the olfactory brain possibly for the first time ever, and setting off the fire alarm…through code.
  • Also, the code is obviously not a complete memory falsifying the experience of the animal receiving it, but close enough that when the real world and this knowledge construct line up, it causes an autonomic emergency deja vu.

I think the “Camera” that could take that memory snapshot is perception/working-memory and the developing chemicals would be concentrations of fight or flight stress hormones that “develop and burn-in” the image. It could also be triggered by something less obvious, like the moment of relief at reaching safety, with the adrenaline fading and your little squirrel heart going like mad. That could prompt a rewind and transcription of the last minute of memory. Who the hell knows?

2, 3 & 4. I imagine the salient details are the Bold and Italic sensations of that experience, the ones that loom and glow in memory as you look back on it, momentarily experienced again. Long term memory is the most economical way to retain this information and would occur naturally. Perhaps mentally reliving the event (including within dreams) a critical number of times prioritizes passing it forward.

5. I got nothing.

It seems certain to me that many classic human knee-jerk fears like spiders, toadstools and snakes are among our deeply reinforced examples of this process. And that brings up some issues closer to home. Presumably, every human baby is born with some of these “presets”. It seems like the nearly global ones must become default elements of our standard inheritance. Is there some process that triggers the elevation of a methylation memory to DNA proper? Is there some tipping point of reinforcement that causes that? Like if PARENT has a trauma experience coded and CHILD does too, (as their own direct experience, not passively) would the two copies being present in CHILD pass on the message to GRANDCHILD with more urgency? For example, could two doubly reinforced people merging their four copies at the moment of conception cause a crossover to DNA inheritance? That question is kind of rhetorical, I’m just shaking my head at the amazing possibilities of this system.

Other random questions:

  • Could that kind of double reinforcement play a part in paralyzing phobias?
  • How long does it take from trauma to rewritten gametes? If the survivor conceived the next day would the information be ready?
  • Men replenish sperm at a rate that shows tremendous optimism, and a woman’s eggs are more or less archived, or at least they travel like a slow and stately parade in comparison to sperm. Does this mean these memories are sex-linked?
  • Since our gametes are so different would there have to be separate mechanisms to do the encoding? Do eggs get these “critical updates”?
  • Are there equivalent positive messages about life success, not just skin-of-our-teeth escapes? It makes some sense to me that success heuristics belong in the system too, but would be harder for us to demonstrate experimentally. Perhaps that’s more of a learn by observation thing. Animal parents can demonstrate life skills but can’t demonstrate how to avoid a monster attack.
  • Can these messages be annotated in the trip from say, a grandparent to a grandchild?
  • Could separate, different messages from different parents ever blend and synthesize into something unique?
  • Is there a decay time for these messages? Do they fade across generations if not reinforced? Is there a mechanism protecting normal healthy species behavior from being dangerously rewritten or overridden by these alerts?

In summary, we are talking about an evolutionary mechanism which fills a couple of the gaping holes in Darwinian theory.

A Tautology for a Theory: “Survival of the fittest” is a fugue idea, chasing its tail. The fittest can only be described by their survival. The Darwinian mechanism is really about the elimination of gene-pool competitors leaving “the fittest” still standing and reproducing. Kinky!

Time: There is no mechanism for the fittest to develop their adaptive advantage except endless friggin’ time and lucky mutations. Evolution has happened much faster in reality than jives with Darwin’s crawlingly slow “change through random accident and mutation” story. Instantly this makes much more sense than calling upon eternity to explain your mechanism.

Random Changes: Random mutations have been studied constantly since the theory launched. In an experiment replicated many times, random mutations have been generated in thousands of generations of fruit flies in the lab by radiation. Not a single lucky mutation resulted. No change in that population resulted.

Galapagos finches have fitness-enhancing beaks but no practical way to acquire them. Deprived of support from randomness and eternity, Darwin is an empty lab coat. We have reached a happy upgrade to our thinking.

Evolution is sophisticated, multilayered and complex. It stacks the deck in any way it can. It behaves at the very least, as if strategic. We are arriving at theories that mirror the subtlety of reality. We are finally getting better at this.

 

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Drones aren’t irrelevant in bee society they just aren’t really the kind of people you want to be seen with.

Drones develop from unfertilized eggs and are haploid. Queens and workers develop from fertilized eggs and are diploid.

Virtually all organisms are diploid, an original genetic mix based on sexual reproduction with a mix of genes from mom (xx) and dad (xy). The only males in a beehive are the drones and they do not participate in gathering nectar and other bee jobs, they are there purely to inseminate the queen (queen being a strange word for ovary, apparently) and drones are the offspring of unfertilized eggs.

So drones are haploid, containing no recombination of the previous generation, it is basically a flying gamete and all its sperm are identical. All those identical sperm have only source of genetic information, the unfertilized egg it hatched from. A drone is basically a clever workaround for an egg to make sperm that makes more eggs. But to bees it’s critical that there is as little genetic drift as possible.  As a result, the sister bees who do all the work are more closely related than ordinary sisters, instead of sharing 50 % of genes they share 75 %. More reinforcement for the idea that a hive is a quasi individual. And get this (pulling from wikipedia below) …

Because the male bee technically has only a mother, and no father, it’s genealogical tree is rather interesting. In the first generation there is one member (the male). One generation back there is also one member (the mother). Two generations back there are two members (the mother and father of the mother). Three generations back there are three members. Four back there are five members. That is, the numbers in each generation going back are 1, 1, 2, 3, 5, 8, … —the Fibonacci Sequence.
bee

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By  Eva Jablonka and Marion J. Lamb

This is a very well written and succinct paper on various kind of inheritance that challenge the Darwinian “Modern Synthesis” model. If you are a Biology nerd you might enjoy it, otherwise it’s here for me to cite certain parts of without directing people to other websites whose link addresses may change.

The address directly below is the paper via website and the link below that is to a PDF hosted here.

http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572008000300001 

Soft inheritance_ challenging the modern synthesis

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A Google assisted remake of Powers of 10. Nicely done, about 3 minutes long. Maya is the Sanskrit word for illusion in Hinduism and Buddhism. It originally meant “To measure”.  I don’t necessarily believe the “we’re living in a simulation” theory but if we are, the farthest out and farthest in moments in the video would be a pair of very effective walls defining the edges.

 

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Arguments against Darwin generally come with theology as the endgame. It reminds me of the artificially intelligent toaster on Red Dwarf; it would engage the crew in deep philosophical chats which all came down to asking if they’d like some toast. My argument against Darwin is his insufficiency. Charles Darwin is the Sigmund Freud of evolutionary theory. His role was groundbreaking and important but his theory is primitive and wrong seen from today. My last article described the cronyism that rewarded him with this iconic status. I don’t know that his name would even be included in our current view of evolutionary theory were it not a battlement that must not be surrendered. Neo Darwinism is essentially Fort Darwin in the middle of extreme Born-again territory. This understandably makes us close ranks despite our differences, but when our wagons are in a circle it’s a sure thing they aren’t going anywhere.

Adding to the situation are the whole constellation of behaviors Thomas Kuhn outlined in The Structure of Scientific Revolutions. There is a naturally conservative and reticent approach among scientific professionals. First, there is the paradigm of our moment which is built on all the earlier work in our field. There MUST be a foundation and things that call that foundation into question are not likely to be welcomed with open arms. If something truly and suddenly proved the state of a discipline wrong, at one level it would be a triumph and at another, a tragedy. It would crash and trash much current research and practice. Jobs would be lost and it would be necessary to fall back to the last critical turning point before starting again from more basic principles. Finally, there tends to be a generational transition; the hard heads often have to age out of the system before a new theory is truly accepted.

Fortunately due to the power of the scientific method it’s extremely rare for a large theoretical collapse. However, it IS in the nature of research moving forward that new principles will be uncovered which are so RIGHT that earlier paradigms are wrong in comparison. It can be sudden or through long diligent efforts but all research will look like alchemy from a distant enough point. Still, it seems unfair to earlier scientific explorers who may be wrong by the light of today, but were as right as possible in their own time. A little generosity hurts no one. Lamarck was about the most correct person on earth about his subject at the time of his writing. Darwin and Wallace likewise, let’s grant them all winner status without faulting them for not being perfect and not staying current long after their time.

Some basic problems with Darwinism

  1. It’s a tautology (circular logic): Survival of the fittest means the fittest are the ones who survive. What exactly is fitness? Something that apparently is present in survivors.
  2. It describes a negative feedback (we could call it “natural elimination”) but not a positive feedback.  Or perhaps only a negative-positive feedback which is really just a distinction without a difference. We see why some die, but why do others change and continue to change? 
  3. No helpful mutation in an individual would be reinforced naturally in the next generation, each would be diluted.
  4. There is no evidence from long term well constructed studies of the kind of random helpful mutations Darwinism requires even in the groups subjected to more mutagens.
  5. The fallback explanation of an unimaginable time scale as the missing piece that completes the puzzle is insufficient to close the gaps we find.

Both Wallace and Lamarck believed in some principle that guided evolution generally toward more success on average. Almost as if the infinite monkeys at typewriters had automatic spelling and grammar check turned on. And perhaps an app that edited out utter nonsense. This is closer to what life on earth looks and feels like…but to this day we have no means of identifying and studying such a principle. Therefore it is unscientific not in the sense of being wrong, just by being un-measurable and undetectable. In his time, Dmitri Mendeleev (who imagined the periodic table)  predicted as yet undiscovered elements because within the framework he was using there were gaps in significant places. Logically, he thought,  there should be something in that spot. That’s how I feel about the missing mechanisms in evolutionary theory. I suspect they are there because the current theory is a tiny sheet that does not cover this bed.

The one interesting breakthrough that seems to be in this class of guiding principles is epigenetic or soft inheritance. It’s very new but means of positive feedbacks leading to positive variation are becoming visible in this field and its many developing subdisciplines. We find information across generations, and the experiences of parents affecting the phenome of the children. Wallace and Lamarck are being reconsidered. I think they should be granted full equality with Darwin as founders.

We shouldn’t regularly act from fear of being compromised by theology if we budge from an earlier spot. It’s Theology that never budges with it’s hand full of supposed aces. Science moves, not impulsively but empirically. Our position so long after Darwin, is blessed with a million knowings he didn’t have a available, but relative to the future we are just as wrong and insufficient as he is to us. It can’t be helped. Or perhaps the only help is accepting and remembering it. It won’t help us measure what we can’t detect but it may help us think in less black and white terms and to look for meaningful gaps. The undetectable of today is the foundation of the theory tomorrow.

 

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