Confirmation of aspects of modern biology

[eehiram]

The following summary is derived from my 2004 biology textbook:
Biology: concepts and applications, 5th edition, by Cecie Starr, published by Brooks/Cole, Thomson Learning.

Given that macroevolution has not been observed directly by humans in recent centuries since the Renaissance, several other aspects of biology connected to evolution have been confirmed. Since Watson and Crick's DNA double helix paper in 1953: microevolution, biotechnology, bioengineering, biometrics, molecular biology, biochemistry, organic chemistry, genetics of DNA and RNA, human genome project (2002), et al. have been confirmed and become established branches of scientific knowledge and departments of academia and schooling.

A few questions remain in macroevolution, such as: abiogenesis (proteins versus nucleotides versus simpler molecules, simple versus complex), anthropic principle, organizing principle (including: exponential progression of dis-tropic organization of biological beings), small collection of hominid remains, some mysterious mass extinctions, etcetera.

Is my summary correct? Is it out-of-date by 2013? I've noticed some updates on abiogenesis, for example...

 

[Pythagorean]

I think its hard to comment on something like this. Can you ask a more specific question? Or maybe ask about one subject at a time?

 

[eehiram]

Thank you for a response! I see that I should focus on one question at a time.
I would like to focus on: Early on life, before the formation of cells. I've noticed some recent developments since the standard explanations of:
gene-first: RNA world
Alexander Oparin's metabolism-first: deep sea thermal vents
meteorites with 90 different amino acids

The recent theory regarding the origin of life appears to be based on:
the origin of the homochirality of amino acids and sugars
I'm having a difficult time in my first attempt to find a peer-reviewed article on http://ip-science.thomsonreuters.com/mjl/ about "origin of the homochirality of amino acids and sugars". Hopefully you are already familiar with this recent development in evolutionary biology.

Can you share any updates on this new field of research?

 

[eehiram]

Alright, since you didn't seem to reply to my narrowing down to the new conjecture on "origin of the homochirality of amino acids and sugars" as an explanation for early life before the formation of cells, here is an easy slam dunk:

Microevolution has indeed been confirmed and observed to occur millions of times over, right? This micro scale of evolution is no longer questioned at all by anyone who is sane and in their right mind and informed of the massive amount of direct scientific observations and data.

Am I correct?

 

[Ygggdrasil]

In the big picture of things, there have been no huge advances in the past decade surrounding the ideas of abiogenesis. There have been a number of exciting studies published in the intervening years exploring and demonstrating ideas about how certain aspects of abiogenesis and the early evolution of life may have proceeded, but nothing that has definitively changed our still very murky view of the process. This is still very much an open question.

On the topic of the origin of homochirality, here's a recent review from Donna Blackmond at the Scripps Research Institute: http://dx.doi.org/10.1098/rstb.2011.0130

With regard to microevolution, a number of experiments have directly observed microevolution in the lab (for example, the Lenski long term evolution experiment which has arguably also produced an example of speciation) and in nature. There are still many open questions about the mechanisms of how microevolution comes about (for example, how do the biophysical properties proteins and their interactions within the cell affect the 'evolvability' of these proteins and to what extent can we use these properties to predict their evolution), but the question is not whether microevolution occurs but how it occurs.

 

[eehiram]

Thank you kindly for responding to both questions! I appreciate your taking the time to answer. I will check the links and respond later, as I have to limit my daily computer access.

I'm glad that you were able to include a recent link on the origin of homochirality. In my humble junior college opinion, this seems to me to be a promising step forward, even if it is ultimately not the true origin of life either, and ends up being added to the list of candidates on the road to abiogenesis.

Unfortunately, I have not taken a class on microevolution, so I won't ask you to replace the material. I will try to use some summaries and do my best in writing my posts.

Thank you again for your patience. I hope that I can ask some questions that are outside-the-scope of my biology class; and ask some advanced questions typically answered later, such as in routine upper division or graduate classes.

 

[Ygggdrasil]

On the issue of abiogenesis, the current issue of Science has a profile on Jack Szostak, who has done some nice work exploring the possible mechanisms for the origin of life:

Szostak, a molecular biologist at Harvard University and Massachusetts General Hospital in Boston, has already accomplished some spectacular science. He shared the 2009 Nobel Prize in physiology or medicine for helping to reveal the role of telomeres, the end bits of chromosomes that help protect genetic instructions during cell division. But more than a decade ago, Szostak shifted his lab's focus to exploring how life on Earth may have gotten its start. He would dearly love to know the recipe for the primordial soup in which it all began some 4 billion years ago. That recipe is almost assuredly lost to history. "We don't have a time machine," Szostak says. "We can't go back."

So he hopes to do the next best thing: fiddle around with a few ingredients of his own and watch as they spontaneously assemble themselves into genes inside simplified cells that copy themselves and demonstrate the first emergent signs of Darwinian evolution. The origin of life. Again. Only this time in a lab.

http://www.sciencemag.org/content/342/6162/1032.full

 

[eehiram]

Thank you for the links. I'm sorry about my delay. Here is my response:

1. The origins of biological homochirality article
As I have tried to read and understand the article, with its helpful introduction, there seems to be a conflict between the easier path and the harder path:

i.The easier path would have a dominant enantiometer at the outset, of which the dominance would be sustained and increased.
ii.The harder path seems to me to be the racemic prebiotic world, with equal parts of both enantiometers.

As the classical historical cases of biology would have it, the harder path is the more relevant to Earth's actual prebiotic conditions, whereas the easier path seems to help as a intermediate stepping stone to figure out biological homochirality (manipulation, investigation, etcetera).

'Symmetry breaking' is the term for the generation of an imbalance between the enantiomeric molecules. The equation cited is ee = (R - S) / (R + S), where R = concentration of right hand molecules, and S = concentration of left hand molecules.

Although broken symmetry could occur by chance, to sustain broken symmetry would require amplification. Otherwise the small, transient fluctuations would be statistically likely to tend to return to the racemic state. Thus, sustaining enantioenrichment requires an amplification mechanism.

Section #2. The easier path is described in the section #2, on Autocatalysis, which is positioned far from equilibrium at the outset. However, to be relevant, this section #2 tends to describe successes in laboratory experimentation that began close to equilibrium and ended with heavy dominance for the favored enantiometer.

(In my own humble estimate, this non-racemic analysis may be instructive, inspiring, hopeful; but not necessarily relevant to the actual historical prebiotic Earth.)

Section #3. The harder path is described in section #3, entitled Physical Models. However, 2 easy cases are considered for the purpose of staying positive:

a) Racemic compounds, which are more prevalent on planet Earth than 10:1; however, only an easy case where symmetry breaking occurs is described.

b) Conglomerates, where separate crystals are composed of each of the two enantiometers, and the two enantiometers do not have the chance to interact.

Section #4. 'Chiral Amnesia' Model. In this section, the crystals of enantiometers in equilibrium evolved inexorably and randomly into one single enantiomorphic solid. The molecules from the crystals on the one hand become part of the crystal on the other hand; thus they suffer from 'chiral amnesia'.

However, if I read the section correctly, there is still no reason to prefer either of the two enantiometers at the outset. An initial surge or fluctuation would seem to be required, once again making the path more difficult.

Section #5. Crystal Engineering Model.
This section ends with the hopeful note:

These studies suggest a general and facile route to homochirality that may have prebiotic relevance. Cycles of rain and evaporation create pools containing a small initial imbalance of amino acid enantiomers and appropriate hydrogen-bonding partner molecules that may form insoluble crystals. The resulting solution of enantioenriched molecules might then serve as efficient asymmetric catalysts or as building blocks themselves for construction of the complex molecules required for recognition, replication and ultimately for the chemical basis of life.

Section #6. Comparison of Physical Models. This overview considers the different models considered, which made me think of my idea that the easier path is more accessible to analysis, yet the harder path is more relevant to conditions on actual historical prebiotic Earth. For example, according to this section, chiral amnesia (part of the easier path) is only relevant to about 10% of known chiral compounds on Earth.

One problem seems to have emerged: symmetry breaking with the presumption of equilibrium on racemic prebiotic Earth. For the sake of brevity, the statistical analysis of fluctuations cancelling each other out is not needed here. Other problems are probably also salient, but this is enough to be instructive to me for now.

 

[eehiram]

2. I would like to post a response about the Lenski long term evolution experiment and microevolution, but will have to do so later, as I have to leave now.

 

[eehiram]

2. Link to thread on these forums about Lenski long term evolution experiment.
Thank you for the link. I attempted to read the first post carefully, and I skimmed the rest, as it appears to be a semi-friendly debate.

A brief summary of mine is: in the Lenski long term evolution experiment, bacteria were frozen in a flask. The bacteria were not able to digest citrate, or only able to digest it at a low level. Given time to micro-evolve through generations, the descendants of the bacteria in the flask were able to digest citrate. Thus "time not design" brought the ability to digest citrate. I think this experiment is a good example of direct observation of micro-evolution.

(I apologize for the verbosity of my response to 1. The origins of homochirality article, as I wanted to convey that I had indeed read the entire article.)

 

[eehiram]

3. Science magazine article.
Thank you for the recommendation. I will try to look for it at the library.

 

[Ygggdrasil]

i.The easier path would have a dominant enantiometer at the outset, of which the dominance would be sustained and increased.
ii.The harder path seems to me to be the racemic prebiotic world, with equal parts of both enantiometers.

As the classical historical cases of biology would have it, the harder path is the more relevant to Earth's actual prebiotic conditions, whereas the easier path seems to help as a intermediate stepping stone to figure out biological homochirality (manipulation, investigation, etcetera).

I would not discount the possibility that prebiotic Earth did have a slight enantiomeric excess (ee) of some biologically-important molecules. As Blackmond notes in her review, some meteorites have been found containing slight ee of various organic compounds (it is hypothesized that the excess of right circularly polarized light in this region of the universe could be the reason for the ee of the material in the meteorites), and there are plausible chemical reactions to convert these materials to L-amino acids and D-sugars (see Breslow 2011. A likely possible origin of homochirality in amino acids and sugars on prebiotic earth. Tetrahedron Let. 52: 2028. http://dx.doi.org/10.1016/j.tetlet.2010.08.094 ). Of course, while this paper provides some plausibility for the "easier path," it is by no means correct and you could still be right that prebiotic Earth did have mostly racemic organic molecules and homochirality would have had to evolve along the "harder path."

 

[eehiram]

Good point! I did overlook the extraterrestrial source for a slight enantiomeric excess (ee) in my summary, as I was reluctant to include it, but will do so now: meteorites could have brought the slight ee excess to prebiotic Earth.

From Section #1: Introduction:

Evidence of small enantiomeric excesses in amino acids found in chondritic meteor deposits [2] allows the hypothesis that the initial imbalance is not of our world.

As far as being correct about my description of a historical racemic prebiotic Earth and a need for symmetry breaking being accurate, I do wish not aim so high as to be right. (Thank you for the encouragement, of course.) I merely wanted to extract the problem being glossed over by the positive tone of the article.

I do not want to seem unfair to the biologists working on this difficult problem. And I do not want to take an excessively negative tone for its own sake. Of course the article is kept short, and cannot answer every anticipated question. I merely suspected that the article itself was trying to push for a solution to the problems alluded to in summary in the last section, #6: Comparison of Physical Models, exempli gratia, that expectations for the crystal engineering model may turn out to be too hopeful to explain the initial enantioenrichment of biologically relevant molecules.

And yet, given the brevity, the article sufficiently alludes to abundant other research conducted and underway. It will be exciting to find out new developments in science literature and magazines in the next 10 years.