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LECTURE NOTES
Second Genesis: The Creation of Life Itself. Now I'd like to look at life itself.
Here are the undisputed facts: [READ].
Science has learned a lot about life's inner workings over the past 50 years, since
we uncovered the genetic machinery that every living cell uses to process its
genetic code. About 10 years ago the human genome project found the complete
genetic code for humans and a number of other species for the first time, and more
species are being sequenced almost daily. This work is still in its infancy and will
assuredly result in many new insights, some of which are already coming to
fruition.
My own first thought about all of this is that if the vast complexity of even the
"simplest" life had been known at the time of Darwin, the notion that life arose
naturally from non-living matter would have been dismissed out of hand. It is at
least to Darwin's credit that he spoke out against efforts to make that claim by
Huxley, Haeckel, and many other acolytes for his cause – perhaps he sensed the
naïve and superficial way that these spokesmen attempted to pave over the deep
waters of the beginnings of life.
There are two good reasons why the notion of spontaneous beginnings would never
have taken hold at that time. First, because at the time most universities and
perhaps most scientists were deeply involved in the Christian religion – indeed
most universities were sponsored by the Church, and many of the scholars were
theologically literate or at least had more than a superficial knowledge of Christian
and Biblical teachings. Even most famous skeptics and agnostics of the 19th
Century had a good working knowledge of the Bible. They would have found it
hard to overlook the theological implications in life's beginnings.
Second, because atheism had not yet become a central dogma in political
philosophy – as was to happen in Marxism, Social Darwinism and in some varieties
of Socialism itself. The combination of politics and science is a lethal mixture and
lends itself to external pressure to conform, with temptations for distortion and
demagoguery.
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But in the event, by the time the true complexity of the origin of life was
understood, whole generations of scientists had grown up without much religious
understanding, and in fact with a good deal of hostility to it, so there was little
motivation to resist the pressures of conformity.
To begin things, I'd like to mention a little-remarked conference held by the
National Academy of Sciences in 1998. Maybe you recall NASA's claim in 1996
about discovering "Mars Fossils" in a meteorite picked up in Antarctica. That claim
caused some heartburn within the scientific field – not because of the claim that the
fossils came from Mars, but because the "fossils" seemed too small to be actual
fossils. The result was a 1998 conference titled "Size Limits of Very Small
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Microorganisms." The conference looked at the physical size constraints imposed
by any form of life (not just the sort that we have on earth) taking into
consideration the functions that life must perform. The conference consensus was
that the smallest imaginable form of life would have to have a genetic code
equivalent to at least 200 genes and a DNA of at least 200,000 base pairs, and the
minimum volume to carry out its tasks would be about 1000x larger than the
alleged Mars fossils.†
The implied conclusion is that the Mars objects are artifacts, not fossils, because
they are too small. I don’t believe this was stated in so many words, because of the
delicate political implications – particularly as it involved the powerful, and
politically-connected NASA. Recall the remark I made a minute or so ago about
the lethal mixture of science and politics.
On the whole, I think that this conference and its conclusion were a bit of an
embarassment to the scientific community, so you don't hear much about it – but
you also don't hear much about these "fossils" either. In a short while I will mention
another conference that suffered a similar fate. As Lydia Miller said, the facts were
"removed to a more distant and dimmer region."
The basic problem is that every life form – by which I mean something that is able
to carry on the minimal tasks of life – is phenomenally complex. And this is doubly
true (literally) if the life form must generate its own food from nonorganic sources,
as the first life most certainly would have to do.
For the record, I welcome efforts to find a simpler form of proto-life, because it
would yield new insights into life itself, even if it continues to come a cropper. One
learns from failures as well as successes.
========
* The report is posted on the National Academy of Sciences website at
http://www.nap.edu/openbook.php?isbn=0309066344&page=1. See also Chapter 6. Be warned that the Wikipedia article on the
"Mars Fossil" is a bit enthusiast-driven, and in particular it (remarkably) doesn't even mention the 1998 NAS conference.
See Chapter 6.
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For one thing, every living cell – even the smallest bacterium – uses the SAME
procedures to process its genetic information*, called the Central Dogma†.
[See the handout, which is reproduced in the next four slides].
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* Viruses cannot process their own genetic information, but take over a living cell to do it. Because of this, I do not view viruses
as "living".
† There seems to be a move to restrict this term to refer to the irreversibility of protein genetics: DNA can be used to create a
protein but a protein cannot be used to create DNA. For the usage here, which involves the machinery needed to form proteins
from DNA gene sequences, see http://www.accessexcellence.org/RC/VL/GG/central.php. See also Chapter 6: Components of the
Central Dogma.
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[READ] Note that if the DNA "ladder" is cut apart in the middle, each side
separately copies the entire genetic code, and two faithful copies of the DNA
molecule could be had by completing each rung with its complementary mate (e.g.
A with T). Thus DNA is inherently redundant. All living species and viruses use
this same way to record genetic information†.
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The smallest Bacterial DNA has over 500,000 base pairs, and there is no reason to
believe that the first living species would be substantially simpler.*
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† For technical accuracy, some viruses use RNA rather than DNA. RNA has the same ladder scheme but the nucleotide T
(Thymine) is replaced with U (uracyl).
* The smallest genome known today has about 500 genes and a DNA of 580,000 base pairs (the bacterium genitalia). See "How
Big are Prokaryotic Genomes?" But this bacterium depends on a lot of food provided by its environment. If one considers the
smallest species that can make its own food from inorganic material, the genome size is more than double this. The cyanobacteria
(mentioned later) DNA (Anabaena) is 7.2 million base pairs (bp) and 5,368 genes. See String of Pearls: the genome sequence of
Anabaena. A smaller cyanobacterium, Synechocystis has 3.57 million bp and 3,168 genes. Cyanobacteria are also called bluegreen algae.
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[READ] Actually tRNA has an anticodon (the codon complement), but let's not get
into that today.
[READ] The DNA code is essentially useless without this regulatory machinery –
so it MUST have been in place from the very start. And some of the regulatory
molecules are themselves quite complex, requiring very special and elaborate
construction.
[READ] Perhaps I should say the mRNA is chaperoned away from the DNA. It
doesn't move by itself.
[READ] This picture shows the ribosome attached to the endoplastic reticulum, a
typical characteristic of eukaryotes. We will say something more about the ER
later.
[READ]
This is the Central Dogma, and it is mind-bogglingly complex. Every cell –
whether bacteria or eukaryote – uses the SAME procedures to process its genetic
information. At least 200 genes and 200,000 DNA base pairs are needed just to set
up the machinery to do this.
One of the great benefits in the recent ability to sequence DNA (that is, list all of
the genes and base pairs), is that the potential exists to examine exactly how every
cell function is coded in the DNA. This takes a lot of work beyond the sequencing,
but for one thing it reveals exactly how each species codes the central dogma.
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DNA sequencing has great promise for showing exactly how evolutionary changes
occur in the species – finally returning evolution to the laboratory, where it
belongs, rather than in the hands of the noisy speculators, the modern day Haeckels
and Huxleys of the world. Finally, after a century and a half, the potential exists to
study evolutionary change with scientific rigor.
Next we will talk about some paradoxes in the creation of life. But first, let's take a
short break. BREAK, Part 1 - 50'40"
Now I would like to mention some genuine paradoxes that are involved in the
program of creating life. All of these paradoxes concern logical problems with
producing complex life through purely natural means. In my own view, the
paradoxes are unanswerable, and they amount to sharp points as regards the origin
of life.
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I'll say something about the first three. We already noted the problems of gene
regulation, and will leave it at that, though much, much more could be said.
The Combinatoric Paradox. This was the subject of a conference at Philadelphia's
venerable Wistar Institute in 1966, titled "Mathematical Challenges to the NeoDarwinian Interpretation of Evolution”*. Some of the leading mathematicians and
evolutionary biologists of the day participated in the conference – including the
mathematician Stanislaw Ulam, and biologists Ernst Mayr and George Wald,
names well-known to me – perhaps some of the other participants are equally
famous, but I am less familiar with them. Wald's Scientific American articles on the
"Origin of Life" (published as a booklet in 1954) were one of my first introductions
to the subject.
[READ QUOTE]
The paradox is that it is impossible to assume that random change could produce
from scratch even a few of the critical genes of a living cell. Thus, if natural
evolution did occur then the only plausible conclusion is that it occurred as a result
of some natural laws – but then those natural laws should be the focus of
evolutionary research, not some facile claim that the power of random selection
produced life or species. What are those laws? Where is the laboratory evidence for
them?
The combinatoric paradox has been expressed in many ways, always leading to an
absurd conclusion. Many analogies have been made – how many thousands or
millions of Britannica encyclopedias of information are represented in even a single
moderate-sized gene, how long it would take monkeys typing at a keyboard to
generate one, etc. These remarks are so obvious that nobody makes them any
longer. There simply is no direct response.
I should note that random -- that is, undirected -- evolution becomes increasingly
less plausible as one moves up the chain of species complexity. Bacteria, at the
bottom of the chain, reproduce in great abundance -- it was once said that if the
descendents of a single e-coli survived, in a single day the descendents would bury
the entire earth to a depth of several feet. This fecundity gives undirected evolution
the maximum opportunity to effect changes. At the opposite extreme, the mammals
reproduce very slowly, so opportunities for random change are drastically reduced.
If there is a combinatoric paradox for bacteria, it is a doubly implausible paradox at
the higher end of the chain of life.
========
* Moorhead & Kaplan, Eds., Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution, Wistar Institute
Symposium Monogram No. 5, 1967. Be warned! It is difficult to find a balanced exposition of the "conclusions" of this
symposium on the internet. It seems that the subject polarizes those who are even aware of the mathematical challenge. The point
of the conference is stated by a participant, Dr. Murray Eden in his paper "Inadequacies of Neo-Darwinian Evolution as a
Scientific Theory" as: "It is our contention that if 'random' is given a serious and crucial interpretation from a probabilistic point of
view, the randomness postulate is highly implausible and that an adequate scientific theory of evolution must await the discovery
and elucidation of new natural laws -- physical, physico-chemical and biological." (p. 109)
cf. http://www.roulettestar.com/roulette-betting-systems.php
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The conclusion is: [READ]
There are four responses to this paradox that I have heard.
The silliest (in my view) is the suggestion that life came here from outer space.
Believe it or not, that is the response of more than one rational scientist – including
Fred Hoyle, Carl Sagan, Richard Dawkins and others. If you don't see that this is a
non-serious suggestion then we have to talk – but not right now, because I have to
keep going....
Second is the infinity of universes argument: Any event, however improbable, will
surely occur given enough universes. Or so goes the argument. As a mathematician,
let me say that this is a shameless abuse of the notion of infinity. Carry it to an
extreme, then there are a thousand (or million, or billion) universes in which there
is – right now, this moment – a Kutztown University with students and faculty
enjoying a lecture by a Dr. David C. Bossard. Pardon me if I don't consider this a
serious suggestion. Never mind the violation of copyright laws.
A third response is that we can get around the combinatoric problem by building up
large genes by making small segments and then combining them. This particular
suggestion sounds to me (as a mathematician who specialized in probability) like
the classical fallacy stated as "there is no combination or betting system that will
turn the odds into your favour."* The odds of getting a very low probability result
cannot be helped by any “system”.
The fact is that although some genes do appear to be repeated copies of small
segments, that is not true of most genes.
========
* cf. http://www.roulettestar.com/roulette-betting-systems.php
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The fourth response is what one of the Wistar participants stated: there must be
unknown natural laws. Well, if that is the case, then the evolutionists should get on
with it and find them. Thus far, to the best of my knowledge, the search has come
up pretty empty. [READ NOTE]
The Eigen Paradox. The second hurdle is what is called the Eigen Paradox*, after
its formulator Manfred Eigen in a 1971 paper. In essence this paradox states that a
gene with over 100 base pairs must be accompanied by error-correction code (also
encoded in genes) that is more complex than the original gene.
Without error-correction, the effect of mutations will overwhelm the stability of the
gene. This paradox has been called by Wikipedia "one of the most intractable
puzzles in the study of the origins of life."
I think that this says it as well as anything I could say, so I will leave it at that.
Every budding computer expert soon learns to his chagrin that debugging computer
software always takes more work than writing the original code. That's just a
microcosm of the Eigen Paradox.
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[READ IMPLICATION]
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* Eigen, M. (1971) Self-organization of matter and evolution of biological macromolecules. Naturwissenschaften 58 (10): 465–
523.
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The Levinthal Paradox. The third hurdle is the Levinthal paradox*, after its
formulator Cyrus Levinthal in 1969. The Levinthal paradox has to do with the fact
that proteins, after they are formed by the ribosome, fold into a unique 3dimensional shape, which is essential to carry out the function for which that
protein exists.
The problem is that there are a huge number of ways that a given protein chain
might fold. In fact, for a chain of 100 amino acids, there are as many as 3 198 =
3x1094 ways to fold. Considering that there are only about 10 80 atoms in the entire
universe, picking out a particular folded configuration is like finding a particular
atom in 100 trillion universes. Unless you are much more optimistic than I, I
assume that you agree that this is hopeless.
In actuality, the folding of proteins is partly spontaneous (for not fully understood
reasons) and partly aided by chaperones, which are other molecules whose specific
task is to help proteins to fold into the correct configuration. In Eukaryotes, the
folding frequently occurs in the endoplasmic reticulum. It's anyone's guess how
they "know" which folding is correct. Again, I suppose we have to invoke unknown
"laws."
Summation thus far. I see the complexity of the central dogma and the
mathematical paradoxes as sharp points, and agree that the only way to maintain a
natural origin of life is to postulate some powerful but unknown laws of nature
which result in the achievement of great order and complexity. The obvious
question is, what are these laws, and is there any independent way to demonstrate
that they exist in nature? As I see it, at least at present, the existence of these laws is
a triumph of faith over logic. But the creation narrative is not yet over….
========
Cyrus Levinthal, "How to Fold Graciously" Mossbauer Spectroscopy in Biological Systems: Proceedings.
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Now I'd like to talk about some of the very complex inventions of the first living
species. I've already talked about the central dogma, so I won't say anything further
at this point. [READ]
I'm not interested in arguing whether all of these inventions were needed by the
very first living thing, but that all were needed before the project of making a fit
environment could get into full swing – and that there is evidence that the project
was already in progress very early in the earth's history.
We will say something about each of these in turn.
========
* See Chapter 6, Chapter 7, and Chapter 8.
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Carbon Fixing. The earliest evidence of life on earth is the appearance of
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biological carbon in the very earliest sedimentary rocks – some dated to 3.9 billion
years ago, close to the first time that the earth had finally cooled to below the
water's boiling point and a global ocean had formed. These rocks are pretty scarce
but they do appear in a few places: Western Greenland, Western Australia and
Eastern South Africa near Swaziland.
Biological carbon has a different ratio of two carbon isotopes: Carbon-13 to
Carbon-12 as compared with the ratio in non-biologic carbon. This preferrence for
C-12 is characteristic of the carbon-fixing RuBisCO molecule associated with the
sugar-making operation of photosynthesis.
Today RuBisCO is "the only link between inorganic and organic carbon.†" While it
is probably impossible to state positively that RuBisCO and photosynthesis were
present in the very first living species, they almost certainly were present in the
oldest fossil ever found – chains of cyanobacteria (or closely related bacteria)
discovered by J. William Schopf in Western Australia, dating about 400 million
years later, to 3.465 By ± 5 My.
Rubisco is an exceedingly complex molecule, and how it works is still not fully
known. And yet it – or something quite similar – was around from the very first. A
sharp point.
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† http://csmres.jmu.edu/biology/Bio480/Fall04/group5/plantexp/intro.htm
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Photosynthesis. Photosynthesis is a complex process that uses two different
Chlorophyll molecules. Each of these molecules is optimal for its task – meaning
that scientists know of nothing that could perform better. Ironically the two steps of
photosynthesis require an oxidizing process and a reducing process, respectively,
and in both instances use the optimal approach (as far as is known).
Chlorophyll II (the first step in photosynthesis, but discovered second,
hence the "II") is "the strongest biological oxidizing agent known.*" It
converts light energy into ATP, a phosphate molecule that is the universal
"battery" of all living species. ATP is generated by a complex motor
molecule ATPase. Chlorophyll II harvests hydrogen from water with oxygen
as a waste product.
Chlorophyll I (the second step in photosynthesis) is "the strongest biological
reducing agent known.*" It uses ATP and other products of Chlorophyll II. It
harvests carbon from carbon dioxide (using RuBisCO) and uses the carbon to
form the short sugar chain, Triose (C6 H12 O6). This is the Calvin Cycle, a
very complex process first described in 1950.
[READ QUOTE] – another sharp point. I would say that this comment ranks up
there with Fred Hoyle's remark about monkeying with physics.
The overall photosynthesis system is similar in both bacteria and plants (although
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there are many differences in detail). In Eukaryotes (plants and animals), one of the
cell organelles, the mitochondria, uses ATPase to build ATP for use by the rest of
the cell. The mitochondria consume oxygen and generate carbon dioxide waste in a
somewhat different arrangement from Chlorophyll-II. This is a major reason why
eukaryotes are oxygen users.
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* See Wikipedia articles on P680 and P700. See also Proceedings of the National Academy of Scientists: "According to an
analysis of the cyanobacterial genome (Haselkorn and Johnston (PNAS)) the earliest cyanobacteria already had the light & Calvin
processes for photosynthesis in place. These are two very complex and subtly linked processes and involve many specialized
molecules working together. These are such complex biological processes, that the complexity and early appearance on earth
seems to indicate planning and design." See Mulkidjanian, Koonan, et. al., Cyanobacterial genome core and the Origin of
.
This is a depiction of the ATPase motor molecule. The motor is embedded in a
membrane and powered by protons (H+) passing through it (just like an electrical
motor of our acquaintance uses electrons – with a stator, rotor and other
paraphernalia of motors). The spinning builds up the ATP molecule by adding a
phosphorous to a growing tail. See animations on Wikipedia.
Nitrogen Fixing. No living species can exist without nitrogen, because it is at the
heart of almost every molecule used in the central dogma, including every
nucleotide in DNA itself. The atmosphere has abundant nitrogen gas, but it is
essentially inert as far as most biological processes are concerned.
Photosynthesis (2006) at http://www.pnas.org/content/103/35/13126.full
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Nitrogen Fixing is the process in which the molecule of nitrogen gas (N 2) is broken
apart into two Ammonia (NH3) molecules (and then often further processed into
others compounds). This is a necessary first step to making biological use of
nitrogen, and it is a very difficult, slow, energy-consuming process, because the
triple-bond molecules of nitrogen gas are bound more tightly than almost any other
molecule (I suppose the quadruple bond of C2 would be even tighter, but there is no
such thing as far as I know). There is some ammonia produced in lightning
discharges, but it is not a reliable enough source to provide a useful amount of
nitrogen for early species of life (although conceivably the very first species could
get a faltering start that way). So very early in the history of life on earth, some way
to fix nitrogen had to be created.
The solution is nitrogenase, a unique, exceedingly complex molecule, probably a
motor molecule, which takes 1.2 seconds and 8 cycles to "fix" a single nitrogen
atom†. Across all of life, only certain specialized bacteria can fix nitrogen, and all
of them use essentially the same nitrogenase molecule: it is the only known
biological way to do it – unique across the entire biological spectrum*. It is also
rare: someone estimated that all of the world's supply of nitrogenase would fit in a
moderate-size bucket.
Cyanobacteria – the same bacteria that produced the earth's atmospheric oxygen –
also fix nitrogen in cells called heterocysts that are specialized for this purpose.
Nitrogenase is poisoned by oxygen, so the cells are protected from oxygen
contamination by special means. This is why the normal cell cannot simultaneously
photosynthesize and fix nitrogen. The akinetes shown here are another type of cell
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with tough walls that are used something like spores or seeds to survive under
tough conditions.
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† See Wikipedia article on nitrogenases. The mechanism of nitrogenase is still not well-known. See The Catalytic Mechanism of
Biological Nitrogen Fixation: "the complicated spin structure of the FeMo-cofactor (shown on the right) is difficult – if not
impossible – to describe with standard methods."
* Nitrogenase of course works at normal room temperature and pressure. The only known inorganic way to fix nitrogen – the
Haber process – requires high temperature and extreme pressure.