Lattimer, AST 248, Lecture 14 – p.1/21 infinitesimally : x a . . ax 3 there is both a , the stable minimum + 0 a/ 3 − = 0 x p a< a is slowly increased, the )= =

Development of Complexity a x ( eq equilibrium system moves smoothly to smaller Consider a potential function V When As When stable minimum (dots) and an unstable maximum in the potential. disappears, and for positive, the system moves abruptlynew to equilibrium a very far removed from the old. x • • • • Catastrophe Theory Boolean Networks A logical system composed of units or nodes that can be in either on or off states (analogy, lightbulbs). One could have a system of N nodes, each connected to K other nodes. Whether a node is on or off is determined by the state of the conected neighbors and a set of logical rules. For example, suppose K = 2, so that node A is connected to nodes B and C, and the logical rules are: if B and C are both on or off, then A is turned on. If B is on and C is off or vice versa then A is turned off. Beginning from an initial state, the network takes a step and alters the state of each node, if necessary, to comply with the logical rules. Since some state of the network will eventually repeat an earlier state, the system will eventually enter a repeating cycle. The length of the cycle could be as short as one step (i.e. the system is fixed) or extremely large. A large network will seem to behave chaotically. In between these extremes, Boolean networks show interesting behavior, such as quickly reverting to cyclical behavior, known as an attractor. For example, if N = 100, 000 and K = 2 there are about √N = 316 different cycles, each about 316 steps long. This is surprisingly orderly behavior: out of the 1030,000 possible states, it will end up in one of these 316 cycles. Thus the vast majority of the system’s possible states are never visited after the limit cycle is obtained. As the network goes into a limit cycle, about 70% of the nodes become frozen, with the other 30% randomly varying. When the frozen sea forms marks a phase transition between chaos and order.

Lattimer, AST 248, Lecture 14 – p.2/21 Stuart Kauffman has applied this model to to describe genetic regulatory networks and to the development of complex . He examines how one goes from an undif- ferentiated egg by repeated division to differentiated cell types: red blood cells, retinal cones, etc. Genes are the nodes of a Boolean network and cell types are the attractors or limit cycles; represents a timestep. He reasons that cell specialization is obtained for free from the connectivity rules. The number of genes in humans is about

100,00 and the number of cell types is about 256, close to its square root. This scal- ing also seems to work for other organisms. Furthermore, about 70% of the genes are permanently turned on in all cell types.

Lattimer, AST 248, Lecture 14 – p.3/21 Lattimer, AST 248, Lecture 14 – p.4/21 the time. About tion, of genes duced length. nt being tested for bout 400 nm in t it into l remediation. l vital metabolic y. Mycoplasma was 2 base pairs with a mino acids or lipids. 00 base pairs and 517 ate artifical . ed in a non-viable

How Small Can Organisms Be? high coding density (97%) with many overlapping genes and re pathways are missing; they cannot synthesis nucleotides, a genes. Numerous genes essential for life are missing. Carsonella ruddii contains a circular of 159,66 discovered in a hydrothermal vent, a Mycoplasma is the smallest free-living with 580,0 A study headed by Craig Venter to find the smallest working set It is also planned to create a synthetic chromosome and injec Intent will be to develop a new fuel or agent for environmenta Number of predicted genes is 182, lowest in record. length, and containing 490,885 base pairs. Genes for severa But it has DNA repairand mechanisms . and can carry out DNA replica necessary for an organism tosubjected live to and random reproduce gene successfull knockouts,signs with of each life. knockout muta Roughly onemutant third were of from the genes knockouts that that300 had result genes a seem function to that be was necessary unknown for at survival. with the original genetic material removed to attempt to cre • • • • • • Smallest and Minimal Project Lattimer, AST 248, Lecture 14 – p.5/21 491kbp). lest bacteria, C. ruddi teorite. C. ◦ 170 − = 115 T

Nanobes (160 kbp) Mycoplasma (580 kbp), or archaeum, Nanoarchaeum ( Filamental structures found in rocks andMight sediments be in smallest 1996. form of life, 10 times smaller than theSmallest smal nanobes are 20 nm inDebate diameter. concerning if they contain DNA. Similar to life-like structures in ALH84001, theCommercially Martian interesting me in plastics manufacturing. Recovered from sandstone rock retreived from 3-5 km under oceanis bed 2000 where atm pressure and Could be implicated in somecalcification diseases of and teeth and arterial walls. It is suggested this couldbut be most a biologists new are form doubtful ofthat at life, they this are stage independent life forms. Main argument against, lacking DNA/RNA evidence, is they are simply too small. What can nanobes tell us about life’s origins? • • • • • • • • • • • Lattimer, AST 248, Lecture 14 – p.6/21 xtreme, perhaps you nk ). long time, so they e specialized; hysics of bones and be as small as 20 nm. proves its efficiency of mes murky, indeed. onment; , so a large collection of osome, 18 nm. With RNA dissimilar from the gene nt of a single cell. Nanobes ecome bigger: hat led to . 9 (2000) , of Biosciences 25 . J , Nanjundiah .

Life and Collective Behavior lose all capacity to reproduce or metabolize on your own (thi offers better protection against changes in physicalit envir can invoke division of labor soit that can different prey parts on becom smaller creatures. they can grow rapidly; you can parasitize something which is larger. Carried to an e • • • • • and proteins, a size limit is closer toPerhaps 50–100 each nm. nanobe contains Nanobes only can nanobes a is part actually of necessary the to living be system the functional equivale Evolution occurs whenever an hereditarysurvival change and by its chance reproduction im rate. The obvious route is to b Limits to becoming smaller imposed by the size of a single rib may represent an extreme degree of collective behavior, not Adapted from V swapping () between t The boundary between living organisms and non-life now beco There is always room at the top, but limits are imposed by the p muscles and gravity. But what about becoming smaller? Microbes have been around a must be successful. ld ent levels, 2 Lattimer, AST 248, Lecture 14 – p.7/21 rganelles of rsity over a 40 Myr roplasts); nuclear old DNA size increase O tic life rd. Causes: O 2 l walls, internal and S 2 S. 2 ), connection to development of Earth’s core and magnetic fie 4 in atmosphere, avoidance of “Oxygen Catastrophe” Developm O 2 3

Major Stages of Evolution First chemofossil evidence of life (disuputed) Cambrian Explosion leading to proliferation of dive First microfossil evidence, first evidence for photosynthe Cyanobacteria develop aerobic photosynthesis using H Earliest evidence for multicellular organisms, including Buildup of O Formation of Earth End of Late Heavy Bombardment of inner solar system First photosynthesizers utilized H membrantes, organelles, sexual reproduction, flexiblescaffolding cel (cytoskeleton). Perhaps connected with large bacteria Magnetobacter with o of Eukaryota through endosymbiosis (mitochondria and chlo magnetite (Fe Life was anaerobic, chemoautotrophs, utilize H at the same time. enables identical DNA replication, 1000-f period. Only major period of family diversification in geologic reco genetic complexity, Snowball Earth, absence of predators. 3.5 Gyr 2.7 Gyr 1.2 Gyr 545 Myr 2.4 Gyr 4.5 Gyr 3.9 Gyr 3.85 Gyr 475 Myr Plants develop means to live on land, evolving from algae. 440 Myr First major extinction (Late Ordovician) 400 Myr Amphibians and insects colonize land. 360 Myr Dense Carboniferous forests, resulting in coal and oil. 250 Myr Permian extinction leading to dinosaur domination 210 Myr Late Triassic extinction

200 Myr First charcoal observed in strata, evidence that O2 levels are near present values. 65 Myr K-T extinction of dinosaurs leading to mammalian domination 60 Myr Last common ancestor of primates 7 Myr Hominid develops, last common ancestor of humans, gorillas and chimpanzees 0.2 Myr First human (Homo sapiens) fossils 0.05 Myr Upper Paleolithic Revolution and exosomatic symbols and projectile weapons: emergence of true intelligence? 0.03 Myr Extinction of Neanderthals 0.012 Myr Extinction of Homo floresiensis

Lattimer, AST 248, Lecture 14 – p.8/21 , so = 4 N Lattimer, AST 248, Lecture 14 – p.9/21 ntent, but ly smaller contains junk the total. not contribute to he activation of ntained in a simple air contains two bits of rnatives down to 1 is bable alternatives .) We will use the genome length to measure the information co

Evolution of Information Capacity = 2 DNA that does not seem to contain useful information. It does reading of base-pairs because genesseveral are other often genes regulated in by a t regulatory network. Much of the human genome, as well as other complex organisms, Conversely, DNA contains additional information to that co information content. In humans, the useful DNA is a mere 2% of Amoebae have a genome 80percentage times is that useful of coding. humans but a considerab N 2 • • the information content of alog message that narrows those alte note that this can be misleading: DNA and Information DNA carries information in a computer-like way. Each base-p information (The prior uncertainty is the number of equipro Information and the Nervous System

The nervous system, especially the brain, also contains information, but the storage is more complicated. • The brain contains 10 billion neurons, each connected to 1000 - 10,000 others. • Neuron positions require little information. A part in a billion accuracy requires about 90 bits per neuron or a total of 120 Mbytes (1 byte = 8 bits). The main information is in the connections. We will need the address of each neuron: 10 billion can be stored with 34 bits (234 = 17 billion), plus an additional bit to specify the on/off state of each. Each synapse involves at least 1000 neurons bringing the total to 35,000 bits per synapse. There are 1010 = 10 billion synapses, involving a total of 3.5 1014 bits or nearly· 0.05 petabytes.

Lattimer, AST 248, Lecture 14 – p.10/21 Lattimer, AST 248, Lecture 14 – p.11/21 n a broad rogressive es, there are the progress is asites are a good . method of storing t length. of another factor of 10 in he length of DNA by ormation storage. on to around 10 million example. It might be thattrend. even a majority of lineages have no p undermined. But is a trend observed in all evolutionary lineages? No, par In those lineages that showmany progressive reversals trends and over re-reversals long in tim the shorter term, so that

Information and Evolution • • base-pairs. genome length. overall trend toward increased information content. Initially, DNA was limited by error-rate during reproducti Error-correcting enzymes (proteins) evolved to increase t Increased specialization of cells accounts for an increase Ulitmately, DNA length is limited by chemistryAt to the its same presen time this limitation was reached, an alternative Nervous systems quickly evolved into brain stemsThe and multiple-connectivity brains of neurons vastly increases inf No one can deny that by any method of measurement there has bee about 100. information developed, involving the nervous system. • • • • • • • • Why does information content increase during evolution? A consequence of natural selection. • Random genetic error (mutations), horizontal gene transfer, sexual recombination, and migratory mixing all increase genetic variation, the available alternatives, so they decrease the available information content. • Natural selection is a winnowing of the available alternatives, and thus increases the information content. • Natural selection is thus nonrandom in the direction of improvement (survivability and reproductivity). • Relatively small changes in the genome have produced major differences in organisms. The chimpanzee genome differs from a human’s by about 2%. A qualitative change in intelligence accompanied small quantitative increase. Big brains, tools (chimpanzees, elephants, ravens), culture and linguistic abilities (apes, whales, dolphins) and self-awareness (elephants, dolphins, apes) aren’t uniquely human. The key step might have been the development of projectile weapons and exosomatic symbols: symbolic intelligence (messaging without direct use of body – decorated clothing, jewelry, paintings, ornate weapons). Further dramatic increases in information capacity occur because of civilization • Societal specialization • Language • Technology (tools, books, computers) Lattimer, AST 248, Lecture 14 – p.12/21 Lattimer, AST 248, Lecture 14 – p.13/21

Primate Evolution Lattimer, AST 248, Lecture 14 – p.14/21

Hominid Evolution Lattimer, AST 248, Lecture 14 – p.15/21

Phylogeny Lattimer, AST 248, Lecture 14 – p.16/21 stor lived 50 Myrs ago. y 1 base per 25 Myrs, ice as long as another, but ngth of DNA found in 2 evidence about dates, such es, is necessary. eins studied can hamper calibration.

Molecular Clocks A molecular clock can definitely say that one time periodas is the tw fossil record or sampling over evolutionary timescal the 2 versions are separated by 100 Myrs and their common ance cannot assign fixed times. Calibration against independent Over time, mutations build upspecies in differs DNA by at 4 a bases reliable and rate. the If entire a DNA le length changes b Small population sizes and changes in functionality of prot Lattimer, AST 248, Lecture 14 – p.17/21 a, Kenya or olecular clock and male MRCA). Seems int MRCA, who is ndrial Eve (female are common ancestors ng elapsed time with time when everybody today ffectively tracing the family tree ) of all currently living humans can be MRCA, the most recent individual from which all was about 5400 BC, when all humans can be divided into

Adam and Eve observed genetic changes. Matrilineal: mitochondrial DNA (mtDNA) traces the Mitocho Patrilineal: Y-chromosome traces the Y-chromosomal Adam ( MRCA). Seems to have livedTanzania, about using 140,000 the years molecular ago clock in technique Ethiopi of correlati to have lived about 60,000genetic – marker 90,000 techniques. years ago in Africa using m identical ancestors point • • estimated to have lived only around 3000 BC. The of all living humans. Puthad another the way: same this set is of the ancestors. most recent two groups: those who left no descendants today and those who The most recent common ancestor ( traced genetically by matrilineal andbackward patrilineal in paths, time. e Eventually, the lineages converge. Both female and male MRCAs lived much longer ago than their jo organisms in the group are directly descended S is much Lattimer, AST 248, Lecture 14 – p.18/21 ′ emporaries. S itle of mitochondrial ze of a population bottleneck not remove her status must be no larger than the size of ′ S . The set of all women who were mothers of S and so on: each succeeding set is smaller than ′′ S will contain 1 woman. (each woman typically has more than 1 child). ′ n S , and the size of S ′ S is S

Ancestry (e.g., a plague reduces enormously the number of humans). But none of them left decendents along the matrilineal line. as an ancestor of allEve women. to a But later further individual. deaths This can happens, shift for the example, t during All humans alive today form the set Repeat the proces to form set This woman was not the only woman alive then; she had many cont Once a mitochondrial Eve is established, further births can before. Finally, the set smaller than the size of the members of (each of us has only 1 mother). But it is more likely that the si • • • • Proof that Mitochondrial Eve (orexists. Y-chromosomal Adam) Lattimer, AST 248, Lecture 14 – p.19/21 , and still others ack, unless some me of the MRCA. n was 300 million. is time, one person er of ancestors would billion. 1 ≈ 30 2

Ancestry and the MRCA were not ancestors of anyone living today. was the MRCA. Others were ancestors of some humans but not all It’s estimated to have been about 170 generations back. At th The number of your ancestorsback must into increase the as past. you go The number of ancestors doubles with each generation going b However, the number of humansdecreases on as the you Earth go into the30 generations past. was 900 years ago, when the world’s populatio There is, therefore, a higherthe likelihood, past, as of you finding go anof into individual any who random was person an alive ancestor today. Go back far enough, and it becomes a certainty: this was the ti of the ancestors are duplicated.be After at 30 most generations, numb • • • Lattimer, AST 248, Lecture 14 – p.20/21

MRCA www.pbs.org/wgbh/nova/neanderthals/mtdna.html From Lattimer, AST 248, Lecture 14 – p.21/21 eome intelligent. xtraterrestrial ately from humans ct has been to : Snowball Earth and ences in organisms. plex and/or uish life and new intelligence to develop: canos, continental drift, mly change the direction atmosphere, relatively stable climate. 2 Impacts Supernovae Gamma-ray Bursts

Evolutionary Implications • • • and pace of evolution; inenhance our evolution one because example, events Earth, did theecological not net niches completely effe were exting created. seem to have a limited or gradual impact. Possible exception events: The chimpanzee genome differs from a human’s by about 2%. Even at a microscopic level, evolutionary advantages of com Several significant physical conditions seem necessary for It is a fact of life that major catastrophic events will rando Major terrestrial-based changes, such as earthquakes, vol Sudden catastropic changes seem to be connected to random, e Relatively small changes in the genome produce major differ Although gorillas and chimpanzees have been evolving separ specialized structures imply that they will develop. land, O the Cambrian Explosion. for the same time span (same common ancestor), they have not b Is intelligence the logical outcome of evolution? • • • • • • •