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The Pilgrimage Begins - Ancestor's Tale

Evolve!

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1richardbsmith
Feb 8, 2013, 9:00am Top

I thought it would be good to start a new topic for the first several Rendezvous's. At some point it will probably be good to begin another new topic.

This is topic will begin a reading of The Ancestor's Tale. I think we can discuss here the prologue and the Farmer's and Cro-Magnon's Tale, at least.

2richardbsmith
Edited: Feb 8, 2013, 9:03am Top

I have read that book by Lee Smolin which is mentioned in pages 3-4, the Life of the Cosmos, where black holes are seeds for daughter universes. It left me with the idea that evolution is a basic law of the universe, and that biological evolution is a special case that adds heritability.

3richardbsmith
Edited: Feb 9, 2013, 12:43pm Top

It is a very interesting point made on page 9.

"we human pilgrims pass only about 40 rendezvous points in all, before we hit the origin of life itself"

40 points of confluence separate homo sapiens from the likely bacterium grandma.

That seems to me to be an astoundingly small number.

4MartyBrandon
Feb 9, 2013, 7:02pm Top

>2 richardbsmith: . . . evolution is a basic law of the universe . . .

I think that's the new understanding, though it's not repeated often enough. We very often here that the 2nd law of thermodynamics dictates how, on the whole, entropy increases, but it's seldom mentioned that in the presence of abundant energy evolution by natural selection can bootstrap pockets of complexity.

Scifi fans might enjoy Greg Egan's short story "Crystal Nights" in which scientists, acknowledging that evolution is the only known mechanism for creating an intelligent organism, set about evolving intelligent life in a computer simulation:

http://ttapress.com/553/crystal-nights-by-greg-egan/

5MartyBrandon
Feb 9, 2013, 7:08pm Top

>3 richardbsmith: That seems to me to be an astoundingly small number.

It strikes me as quite amazing as well. I like that Dawkins tells us the approximate number of generations in the past at which rendezvous occurred. Granted a million generations is quite a lot, but it's not an astronomically large figure.

6richardbsmith
Feb 9, 2013, 7:26pm Top

Another point to keep front of mind for me, is that all the pilgrims are currently living species. Each one has undergone evolution from our common ancestor, sufficient to adapt to survival in our modern world.

Today's bacteria have essentially evolved from our same common ancestor over the past 3 Gy, enough evolutionary change to stay successfully adapted to the world as it changed over that time.

I try to picture the changes that the genus Homo has undergone in the last couple million years, to envision similar change in all species that are presently alive today.

7richardbsmith
Edited: Feb 9, 2013, 10:32pm Top

I am having a bit of trouble grasping the earlier point, past the common ancestor, at which everybody is either a common ancestor or has no surviving descendants.

Part of my trouble I think is that I am trying to apply this concept to the speciation rendezvous's. Those previous individuals prior to the most common ancestor that do not have a descendant in one species may possibly have a descendant in another species.

It may be that this point about the earlier common ancestors is not a significant point. It just so far has confused me.

This is discussed in the first part of the Tasmanian's Tale.

8MartyBrandon
Feb 10, 2013, 9:26am Top

>7 richardbsmith: I am having a bit of trouble grasping the earlier point, past the common ancestor, at which everybody is either a common ancestor or has no surviving descendants.

I thought this was a little confusing too and would have benefited from a diagram. I think Dawkins is referring to how it might have looked in the very beginning when life first came into existence. We might imagine a soup of proto-organisms like goop in a giant test tube. Presumably all life arose from a sub-population within the big tube. At this early point, the proto-organisms are either part of those that gave rise to everything we see today (each one of these can be considered our common ancestor), or they are in the groups of proto-organisms that died out leaving no surviving descendents.

Rather than one giant test tube, it could be that life arose in several places on the earth and that our lineage displaced all the others. I find this particularly fascinating. Might we still find remnants of one of the other lineages? Does the current lineage of life preclude it from arising in a different form? If not, why hasn't it bootstrapped itself again over the last 3 billion years?

9richardbsmith
Edited: Feb 10, 2013, 1:16pm Top

Similar thoughts about other lineages have also come to my mind.

Some possible reasons that other lineages have not arisen might be that the conditions no longer exist for spontaneous creation of life, the existence of other competing life with a firmer hold on survival, general difficulty in achieving sustainable chain of life.

It seems possible that proto life would have come into existence many times, but only once did it become established. The same forces that bring together the right molecules may almost as quickly destroy them. At some point the right combination formed within a membrane that provided protection from the environment.

It may be difficult to exist as RNA without a protective membrane. Things always seem to point to the cell for the start.

Dawkins though hints at the excitement that would exist around the first new type of life.

10MartyBrandon
Feb 10, 2013, 5:20pm Top

. . . the conditions no longer exist for spontaneous creation of life . . .

That's an interesting idea. We know that microorganisms had a reducing affect for a very long time adding oxygen to the early anaerobic atmosphere. Perhaps anoxic conditions are more favorable. If so, perhaps some of the extreme environments on earth would still be conducive for the process.

It may be difficult to exist as RNA without a protective membrane. . . .

You're familiar with the RNA-world hypothesis? Micelles have been shown to form spontaneously when lipids are added to water, providing a safe haven for fragile RNA molecules. But why aren't the RNA-based progenitors still around? Why did they all give way to DNA-based life? Perhaps there's a sort of platypus-like microorganism waiting to be discovered. We mostly know about bacteria indirectly, by growing colonies in a plate containing some concoction of nutrients. It's thought (at least it was around 10 yrs. ago) that we're capable of growing only a small fraction of the existing bacteria. Maybe some undiscovered variety hails from a completely different lineage, one that stalled at the microorganism phase. Carl Woese had a near-miss when he characterized the Archaeans.

11richardbsmith
Edited: Feb 10, 2013, 5:46pm Top

I am familiar with the RNA world hypothesis as long as being familiar means I have heard of it. I am not able to discuss any nuances or any difficulties with the hypothesis. I somewhat thought it was generally accepted as a likely pathway for abiogenesis.

Part of the conditions for creation of life might also be vast numbers of interactions. Perhaps we might think that vast numbers could be achieved with vast time, say 3 Gy or so, but maybe not. It may take vast numbers in the current time of ample extreme conditions

Plus one of the most significant conditions for the creation of life might be the absence of competition. Life is fragile. Incipient life probably more so.

Perhaps life started many times. And of those many times, it took hold on Eath just once. Among those vast numbers of opportunity, only once. And that was without competition from a superior pre-existing form.

12richardbsmith
Feb 10, 2013, 11:40pm Top

This seems to be an interesting point in Eve's Tale about tracking migration episodes through different haplotypes including mtDNA and Y-DNA.

The non sex DNA haplotypes have older date for the most recent common ancestor, in the 500 Kya range. mtDNA and Y-DNA are from the 140 Kya range. That date is consistent with the dating of Mitochondrial Eve.

Dawkins indicates that there is nothing special about our current Eve. As various blocks of descendants die out, the date for Mitochondrial Eve will advance. Our current Eve will lose her place of eminence.

What is the significance of the persistence of older haplotypes?

It will also be interesting to see what done on a continuing basis with the distinction between genetic and individual heritage. It seems likely to me that such a distinction will not be continued as a main point in subsequent chapters.

13MartyBrandon
Feb 11, 2013, 6:26am Top

>11 richardbsmith:, 12 The RNA-world explains much, and is widely known, but I don't think it has become dogma yet. Was there any mention of panspermia in your astronomy course? My day job is at Goddard Spaceflight Center, and the astrobiologists here talk about that idea often, though it was barely mentioned in biology class. And of course the two ideas aren't mutually exclusive, though the arrival of a meteorite containing complex molecules is one alternative to an RNA-centric intermediary.

Dates derived from molecular evidence are notoriously tricky since they have to assume a certain rate of DNA mutation, which is known to vary considerably (mtDNA, due to its close proximity to reactive radicals mutates 5-10 times more quickly).

An old haplotype would generally be assumed to be evolutionarily restrictive in some way, such that alternative alleles were selected against. The lab I worked in specialized in mitochondrial medicine, and I worked on systems used to assess the the likely contribution of a given DNA variant to a disease phenotype. If a variant caused a change to a very old haplotype, one that we share with distantly related species for example, that was an indication of trouble.

14richardbsmith
Feb 11, 2013, 8:02am Top

We did not discuss the origins of life in the Astronomy course, and panspermia did not come up. There is an astrobiology course going on now, but I did not enroll in it. So far that course is getting less than stellar reviews in the evolution and astronomy discussion forums.

Life may have been brought to Earth in our case, but of course that does not answer the question about life's origins.

A related question that I have asked before is how would the discovery of other life forms impact our survival - what is the chance that a microorganism from another world bring new disease to our world?

Your point about old haplotypes is helpful. I was trying to think how a significant section of DNA might avoid some type of recombination over such a long period. Luck? Especially strong bonds? Close proximity - but if all the genes are close then it could not be especially long, could it?

Your point is that alleles in these haplotypes have heavy selection pressure against their survival? So these DNA section likely experience normal recombination, but typically the genotypes with these sections recombined do not survive?

15Tid
Feb 11, 2013, 6:18pm Top

I've not read the book so forgive my leaping in, in my usual fashion.

I'm constantly surprised how we oxygen breathers have - however remotely - ancestors to whom oxygen was toxic and who mostly died out. Is it too fanciful to imagine a future, long after the direst outcome of climate change for example, when perhaps methane is the dominant atmospheric component, and oxygen breathers have died out to be replaced by methane breathers?

But perhaps I'm speculating outside the scope of this conversation? If so, please tell me so, and I will withdraw to less rarified climes!

16MartyBrandon
Edited: Feb 11, 2013, 7:04pm Top

Stanford's astrobiology course lectures are available through iTunesU. I watched the episodes from one of the 2008 semesters and enjoyed them. It was basically a survey of all the places in the solar system that look promising for the discovery of new life, as well as what can be learned from studying the organisms that live in extreme environments on earth.

https://itunes.apple.com/us/itunes-u/astrobiology-space-exploration/id384233328

Life may have been brought to Earth in our case, but of course that does not answer the question about life's origins.

True, but it greatly expands the possibilities. One of the astrobiology seminars discussed the chemistry that occurs on asteroids in deep space. Though cold, they heat up momentarily due to collisions. The things produced are similar to those in the famous Miller–Urey experiment.

A related question that I have asked before is how would the discovery of other life forms impact our survival - what is the chance that a microorganism from another world bring new disease to our world.

I'm not an immunologist, but I know the general rule of thumb for infectious diseases. Largely, they are host-specific, so it seems quite likely that an alien microorganism would be benign. But who knows what form it might take. Perhaps it has a novel way attacking carbon molecules in general. And when an infectious disease does "jump species" it's often quite deadly (e.g. HIV).

Certain haplotypes do ride along unchanged over time simply by being in very close proximity to a region that's under strong selective pressure, but generally the longer the region of DNA the more likely it is to undergo a recombination event (mtDNA doesn't go through meiotic recombination).

Your point is that alleles in these haplotypes have heavy selection pressure against their survival?
Selection pressure works both ways, i.e. for or against survival. In the clinical I worked in, we were attempting to identify newly acquired variants that were deleterious. Seeing a variant, especially one not found in close relatives, that exists within a highly conserved region of DNA is a smoking gun.

17jjwilson61
Feb 11, 2013, 7:04pm Top

True, but it greatly expands the possibilities.

Not really. All the ingredients of life are available on Earth so there's nothing to be gained by invoking chemicals from space.

18MartyBrandon
Feb 11, 2013, 7:45pm Top

>17 jjwilson61: Meteorites open up the possibility of a far greater scale in both space and time for the process to have occurred. One can then imagine many more ways in which life might be propagated through the cosmos. That's the point.

19richardbsmith
Feb 11, 2013, 8:04pm Top

Thanks for the links to videos about astrobiology Marty. I cannot think of a more exciting prospect than the discover of new life - and whether it is different from our form or similar.

If it is different there would be much to learn about what it means to be alive.

If it is similar, then the question arises in my mind whether we have the same seeding (such as panspermia ideas) or whether we have arisen with separately with similar chemistry (suggesting that life may have limited paths through which to develop).

20richardbsmith
Feb 11, 2013, 8:11pm Top

In the Ergast's Tale, Dawkins discussed the origin of speaking. He mentions different conflicting evidences and theories:

fossils that suggest the speech areas of the brain enlarged about 2 million years ago
skeletons that suggest a lack of capacity for precision breathing
the speech allele in the FOXP2 gene
even, the idea that the language is related to the Great Leap of the Cro Magnon man

Does anyone know of any new developments in the question of the dating of the development of speech?

21jjwilson61
Feb 11, 2013, 11:29pm Top

17> No, because we're just talking about the ingredients of life, not life itself. I haven't seen anything that DNA or anything like it can survive in space.

23MartyBrandon
Feb 12, 2013, 5:41am Top

>19 richardbsmith: I agree, it'd be very profound to find any form of alien life.

24richardbsmith
Feb 12, 2013, 6:38am Top

Marty,
Interesting videos. I may enroll into the astrobiology class. You can enroll in the classes and just audit and download the lesson videos. Watching them at some later point when supposedly there is more time. :)

25MartyBrandon
Feb 12, 2013, 6:39pm Top

>24 richardbsmith: You seem to have a voracious appetite for information Richard. I was content to just view the lectures. I reached concestor 15 today, and was humbled to be reminded of how long our ancestors spent in the "shrew state". Though I have an appreciation of nature, I've never been much of a naturalist. Most of my biological knowledge is about molecules, and I'm enjoying this opportunity to learn something new.

26richardbsmith
Edited: Feb 12, 2013, 6:48pm Top

If you are on concestor 15, then you are much farther than I am. I wonder if others are reading. My pace is a little slowed by time spent on some online courses, but I had no idea that I was so far behind your pace.

I am just starting on rendezvous 1 with our cousins the chimps. I may post here a question about brain size and the ideas that Dawkins posted about dividing lines and how gradual evolution necessarily is.

BTW
The astrobiology course was not accepting new enrollment. I think enrollment was closed after the first quiz deadline. I did register for the next offering TBA.

27MartyBrandon
Feb 13, 2013, 7:11am Top

>26 richardbsmith: The concestors are beginning to blur together a little, so I've got to go back and review the last few. It helps me that some are associated with the arrangement of the ancient landmasses. Learning their configuration is giving me a handhold for the concestors.

I know a bit about the controversies surrounding the rate of evolution.

I think itunesU, and similar projects, are a world-changing endeavor that haven't been widely recognized. Now, anyone in the world with an internet connection can get an MIT education (at least they can see the lectures) for free. I'd expect that the value of a diploma will gradually be replaced by the value of knowing.

28richardbsmith
Feb 13, 2013, 9:54am Top

Education is definitely going to change with this new access given by the MOOC model. Coursera is starting to offer college credits for the same classes I am taking. The classes are difficult - astronomy was crushingly so.

This is my second read of Ancestor's Tale. And I would like to get a handle on the concepts he discusses, as well as an image of the concestors themselves.

I mentioned the points made about brain size and the incremental changes that accumulate to develop into speciation - the difficulty of drawing the line. It is just at some point two extremes of a spectrum are enough different.

Brain size is discusses with its own significance, but also as illustrative of principles with wider applicability, such as accomodating different sizes (3/4 rule), incremental changes and dividing lines, and co-evolution of traits including matching function and form.

This evolution thing is wonderfully intricate.

29Tid
Feb 13, 2013, 5:57pm Top

26

No, I just joined in with the conversation - I don't even know what the Ancestor's Tale course is, even. As for 'concestor', you've got me there!

30richardbsmith
Edited: Feb 13, 2013, 6:48pm Top

Tid,

It is not a course, but a book.

http://www.librarything.com/topic/136314

The talk about a course is just side chatter about some online courses I am doing on Coursera. One of which though coincidently is on evolution.

concestor is a word coined by Dawkins for the book - it means something like a common ancestor species identified or projected which is shared by multiple modern species.

The idea in the book is that we read tales from various common ancestors, concestors, which lead to the one concestor of all life on Earth.

31MartyBrandon
Feb 13, 2013, 7:28pm Top

>28 richardbsmith: You lost me on the brain size. 3/4 rule? Is that in the book?

Species has always been a fuzzy term. Biologists use it pragmatically to denote a group that are likely to couple together to produce viable offspring. Note that two species might be biologically capable of producing offspring, only they normally wouldn't have the opportunity because of physical, temporal, or behavioral separation. Over time they diverge more and more until the offspring are no longer viable or they can't mate at all.

32richardbsmith
Feb 13, 2013, 8:40pm Top

The 3/4 is a recurring slope of a relation between increases body size and organ size. In the Handyman's Tale, pg 77-85. Specifically the pg 81 ad 82, although I don't know that our pages are the same.

The paragraph beginning 'Suppose and elephant sized animal" through the next 3 or 4 paragraphs.

It is apparently a common correlation factor for comparing different scales among plants and animals. In this tale is focuses on brain size compared to body size.

33richardbsmith
Feb 14, 2013, 6:56am Top

That section continues to discuss EQ, a braininess quotient. the brain capacity relative to an expected size given total animal size. Homo genus is higher than typical mammals, suggesting an evolving larger brain.

The graph on p84 shows H sapiens brain 6x larger than expected.

The trend for the genus is ever increasing brain size, which of course suggests that in another few million years the genus will have even larger brains. Not an new idea but one very clearly seen and explained in that graph.

34MartyBrandon
Feb 14, 2013, 7:02am Top

>32 richardbsmith: Thanks Richard. I have an electronic version of the book given to me some years back, and I don't see the part you're describing. The book is divided into 20 files, so I didn't realize it was abridged. Wikipedia filled in the gap though:

http://en.wikipedia.org/wiki/Kleiber%27s_law

35richardbsmith
Feb 14, 2013, 7:17am Top

Wow. Dawkins just introduces the ratio and indicates that it shows up a lot. I did not think to search for information on that ratio. I will look over the wiki article and see if it requires a higher EQ ratio than I have. :)

36jjwilson61
Feb 14, 2013, 11:26am Top

The trend for the genus is ever increasing brain size, which of course suggests that in another few million years the genus will have even larger brains

Not really. Evolution doesn't have momentum and the evolutionary pressures today are much different than they were a million years ago so I imagine that the trend could very well have veered to a different course.

37MartyBrandon
Feb 14, 2013, 7:38pm Top

>35 richardbsmith: A number of these types of correlations pop-up in biology, and I remember Nick Lane saying something profound about how one impacted cellular evolution. Have to try and look that up. And a bigger brain would certainly be okay with me.

38MartyBrandon
Feb 16, 2013, 7:46am Top

Richard, any interesting discoveries about brain development?

Haven't had any reading time the last couple of days, but I listened to Brian Cox discuss the origins of life on the BBC's Discover Wildlife podcast.

http://www.discoverwildlife.com/podcasts

39richardbsmith
Feb 18, 2013, 1:56pm Top

Marty,

I wonder if anyone else is reading along. I have been somewhat slowed by some of the courses - I am taking the evolution course, and also a calculus and a philosophy course. I had some midterm exams this week. And now there is an electromagnetism course starting today.

But I have read through the Gibbons concestor.

The question of bipedality vs tree living in that concestor is very interesting. Just how distinguishing for early humans was bipedality.

40johnabell
Edited: Mar 3, 2013, 11:44pm Top

This message has been deleted by its author.

41qebo
Mar 5, 2013, 7:44am Top

39: I'm nearly done, but RL has been getting in the way of LT.

42MartyBrandon
Mar 8, 2013, 8:52pm Top

I got a little distracted also, but picked it back up again yesterday.

43richardbsmith
Mar 29, 2013, 11:40am Top

I am close to finishing that evolution course, but have also started a biology course led by Eric Lander from MIT, recent recepient of the Breakthrough Prize in Life Sciences, among many other distinguishments.

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