We’ve often heard this claim from creationists: “there is no way for genetics to cause an increase in complexity without a designer!”. A recent example has been Michael Egnor’s obtuse caterwauling about it. We, including myself, usually respond in the same way: of course it can. And then we list examples of observations that support the obviously true conclusion that you can get increases in genetic information over time: we talk about gene duplication, gene families, pseudogenes, etc., all well-documented manifestations of natural processes that increase the genetic content of the organism. It happens, it’s clear and simple, get over it, creationists.
Maybe we’ve been missing the point all along, though. The premise of that question from the creationists is what they consider a self-evident fact: that evolution posits a steady increase in complexity from bacteria to Homo sapiens, the deep-rooted idea of the scala natura, a ladder of complexity from simple to complex. Their argument is that the ladder cannot be climbed, and our response is usually, “sure it can, watch!” when perhaps a better answer, one that is even more damaging to their ideology, is that there is no ladder to climb.
That’s a tougher answer to explain, though, and what makes it even more difficult is that there is a long scientific tradition of pretending the ladder is there. Larry Moran has an excellent article on this problem (Alex has a different perspective), and I want to expand on it a little more.
Larry points out that there’s an awful lot of effort being put into coming up with excuses for an observation, that the number of human genes isn’t that much greater than the number of genes in a fly. He has usefully categorized seven different kinds of rationalizations that people use to try to inflate the complexity of our genome, in the hopes of somehow reassuring themselves that they can explain our much, much greater complexity than a fly or a nematode or a mouse.
- Alternative Splicing: We may not have many more genes than a fruit fly but our genes can be rearranged in many different ways and this accounts for why we are much more complex. We have only 25,000 genes but through the magic of alternative splicing we can make 100,000 different proteins. That makes us almost ten times more complex than a fruit fly. (Assuming they don’t do alternative splicing.)
- Small RNAs: Scientists have miscalculated the number of genes by focusing only on protein encoding genes. Our genome actually contains tens of thousands of genes for small regulatory RNAs. These small RNA molecules combine in very complex ways to control the expression of the more traditional genes. This extra layer of complexity, not found in simple organisms, is what explains the Deflated Ego Problem.
- Pseudogenes: The human genome contains thousands of apparently inactive genes called pseudogenes. Many of these genes are not extinct genes, as is commonly believed. Instead, they are genes-in-waiting. The complexity of humans is explained by invoking ways of tapping into this reserve to create new genes very quickly.
- Transposons: The human genome is full of transposons but most scientists ignore them and don’t count them in the number of genes. However, transposons are constantly jumping around in the genome and when they land next to a gene they can change it or cause it to be expressed differently. This vast pool of transposons makes our genome much more complicated than that of the simple species. This genome complexity is what’s responsible for making humans more complex.
- Regulatory Sequences: The human genome is huge compared to those of the simple species. All this extra DNA is due to increases in the number of regulatory sequences that control gene expression. We don’t have many more protein-encoding regions but we have a much more complex system of regulating the expression of proteins. Thus, the fact that we are more complex than a fruit fly is not due to more genes but to more complex systems of regulation.
- The Unspecified Anti-Junk Argument: We don’t know exactly how to explain the Deflated Ego Problem but it must have something to do with so-called “junk” DNA. There’s more and more evidence that junk DNA has a function. It’s almost certain that there’s something hidden in the extra-genic DNA that will explain our complexity. We’ll find it eventually.
- Post-translational Modification: Proteins can be expensively modified in various was after they are synthesized. The modifications, such as phosphorylation, glycosylation, editing, etc., give rise to variants with different functions. In this way, the 25,000 primary protein products can actually be modified to make a set of enzymes with several hundred thousand different functions. That explains why we are so much more complicated than worms even though we have similar numbers of genes.
It’s important to note that these are not bogus phenomena—there is alternative splicing and small RNAs are important and regulatory sequence is immensely important (especially if you ask a developmental biologist), and so forth. He’s not trying to make these explanations go away (although maybe the junk DNA excuse is feeble enough that it should be ignored) — the point is that these mechanisms do not address the question. These phenomena are going on in all of those so-called “simpler” organisms, too—it’s not as if the hominid lineage was blessed with alternative splicing enzymes and miRNAs and beetles were damned to trifling insignificance without them. It’s certainly not as if insects lack the sophisticated mechanisms of gene regulation found in mammals.
Larry’s answer is the same as mine, and it cuts right through the whole mess of tangled explanations: these are non-answers to a non-problem. The problem goes away if you stop assuming that people are more complicated than mice. With some exceptions, you’re asking the wrong questions if you’re talking about complexity.
I like to compare humans with chimpanzees—are we more complex? I don’t think there is any way to say that we are. We have about the same number of genes and a genome that is about the same size and that is organized in a roughly similar way. There is some speculation about the differences in our genomes that lead to the obvious differences in our morphology, but they don’t postulate any increases in complexity. There are, for instances, genes like ASPM that are found in both species (and in flies!) and are known to act as regulators of mitotic activity. If the form of ASPM in humans has a few nucleotide changes in it that allows certain regions of the brain to engage in a few more divisions than occurs in a chimp, it increases the size of that region, but is that an increase in complexity? If other genes have changes in their regulatory regions (I told you those are important) that switch them on and off at different times in development, allowing for timing shifts that emphasize the growth of certain structures over others, is that an increase in complexity?
I would say no. Those are differences, not increases. With a genome of tens of thousands of genes, there is the potential for a colossal amount of diversity, and what’s going on in metazoan clades is not really an addition of new information, but an exploration of the potential morphogenetic space. Think of 10,000 genes as really representing 10,000 dimensions, with individual species occupying small compact clouds in that immense space, flies off in one corner, us in another, with the chimpanzee cloud somewhere nearby. It’s a misrepresentation of the problem to try and argue that we humans need a significantly greater number of bits to define our position than do flies or chimpanzees.
One thing that has long bugged me is that there’s a fair amount of argument in the scientific literature that presupposes a trend of increasing informational complexity in metazoan lineages — Larry is pointing out some current issues in modern genomics that are afflicted with this assumption, but this is actually an issue that has been simmering in my head for some time now, and I’ve written on it before.
Long before. Before the blog. Back in the ancient days of usenet. On a dusty parchment scroll archived in the great data banks of Google, there is a post from January of 2000 with an argument I will now reconstruct on this vastly more modern medium.
Here’s where I begin. Way back even before usenet, when I was a lowly undergraduate, I read JT Bonner’s On Development, which was one of those dangerous books that lead one down whole new intellectual paths. He has a long discussion on complexity in one of the early chapters, which revealed that this is one of those really hard problems. There are so many different ways to measure complexity that one ends up just throwing up one’s hands and declaring that everything in biology is complex, which is just fine. That chart on the right is one of many ways he tried to look at biological complexity. It plots organism volume and total cell number against a rough estimate of the number of cell types, and concludes that they’re roughly correlated. If you have lots and lots of cells, you have greater potential and greater need for a division of labor, so maybe that’s all that is going on here. It’s a sensible answer, and Bonner’s treatment of this problem is among the best I’ve read since, but even at my tender and relatively unschooled age I could see some problems. A human is significantly smaller than a sequoia, for instance, but I suspected we’d have approximately the same number of cell types as a whale, which would make a mess of the upper end of that graph. And how do you count cell types, anyway? That ordinal axis is awfully fuzzily defined, and there seems to be some selective presentation of the data to just those instances that make a nice line.
Much later, I read Stuart Kauffman’s At Home in the Universe. It’s an excellent and thought-provoking book, but the attempt to measure complexity in number of cell types reared it’s bleary-eyed head again. Here’s the worst piece of data in the whole book. It’s comparing ‘measurements’ from biology with the results of some interesting computer simulations he was doing. He had models where he’d vary the number of simulated interacting genes, and observe that the simulations would all converge on a much smaller number of basins of attraction, so he’s equating number of model genes with the quantity of DNA in a cell, and the number of attractors to the number of cell types, and showing that both simulation and biology show roughly similar trends.
This is a horrible graph with many problems that completely invalidate its utility. Number of genes and quantity of DNA are not the same thing, especially when you note that “bacteria” (there is only one kind, of course, I cynically suggest) with negligible junk DNA and humans with huge amounts of junk are plotted on that same axis. The data are also selective: where are the ferns and amphibians, which have so much DNA that they would be placed on the far right of the scale? And then there is the mysterious “number of cell types” parameter, the source of which is not explained. We are told that man has 256 cell types and flies have 60, though, which struck me as unlikely and low, especially when they are being equated with gene regulatory states. Mainly, it seemed like a parameter with values selected to put humans at the high end and bacteria at the low.
The text of the book does itself no favors when it announces the accuracy of the simulation by pointing out that it returns approximately the same number of cell types — 317 — as are found in humans — 256, which I find dubious — when it uses the same number of genes as are found in humans — 100,000. Ooops. The book was written in 1995, but still, there wasn’t good reason to think we had that many genes even then. It’s also strange that the graph shows the point for Man corresponding to about 700,000 model genes. When no hard numbers are to be had, the values for your analysis seem to become infinitely malleable.
Anyway, I finished the book thinking Kauffman had some interesting ideas, but his grounding in biology was shaky to say the least.
Then Glenn Morton led me to a paper by Valentine and others. For those who don’t know of him, Valentine is a brilliant evolutionary biologist, and I will freely admit that he’s much, much smarter than I am, but this paper was baloney. It specifically tries to assemble a picture of increasing complexity of metazoans over evolutionary history using cell type number as a measure of complexity. At the very least, though, it gives a citation for the source of all of those various estimates of cell type number: a paper on taxonomic biochemistry from 1964, by Sneath. I am sad to say that I have not been able to track down a copy of this fairly obscure paper from a very specialized book (I have received synopses from people who have), but there is a hint of the methodology in the Valentine paper: Sneath was plotting “estimates of cell type number against measures of DNA content of the haploid genomes of a range of organisms including metazoan phyla”, and he concluded that they were proportional. Right there, we know that this is both crude and wrong; there is no correlation of complexity and DNA content (unless we’re prepared to admit that frogs and ferns are the most complex organisms of all time). The Valentine paper briefly acknowledges this problem, then ignores it, to produce this chart:
Glenn Morton also extracted estimated numbers from the chart, if you prefer your data tabular.
| # cell types | age (mya) | |
| Porifera | 10 | 570 |
| Cnidaria | 14 | 560 |
| Hæmocoelic Bilaterian | 30 | 560 |
| Arthropoda | 51 | 530 |
| Echinodermata, Annelids | 39 | 525 |
| Agnatha | 64 | 510 |
| Cephalopoda | 75 | 500 |
| Actinopterygii | 132 | 400 |
| Amphibia | 150 | 330 |
| Diapsida | 154 | 300 |
| Aves | 187 | 150 |
| Hominidae | 210 | 5 |
It’s the march of rising complexity from sponges to man! It’s a beautiful example of garbage in, garbage out.
Almost all of the numbers for cell types are taken from Sneath, and are listed in an appendix at the end. Most of the exceptions are at the low end of the scale, the porifera and cnidaria, where cell type numbers are enumerable, and for the hominidae, which is taken from a molecular biology textbook (and I have my doubts about their quality, too). Sneath’s numbers are flagged with an asterisk, to indicate that they are “estimates not documented by lists of cell types or by references to published histological descriptions”—in other words, they’re unverifiable guesses, and the Sneath paper is the dead end in a search for the source of the estimates. I hate to say it, but these are bad data. Almost every point’s position on the Y-axis is noise — noise colored by an assumption that, for instance, a ray-finned fish must be simpler in organization than a bird. And I don’t trust it a bit.
Another peculiarity is the choice of hominids as the terminal point. I don’t know of any evidence that we have more cell types than a horse or a kangaroo, and since these are all rough estimates anyway, it would have been more appropriate to use a number for “mammals”—which would have pushed that data point a hundred million years to the left. There’s wobble in both the X and Y coordinates of each data point, which makes that line even more worrisome. This paper is an exercise in Markovian modeling of how random variance in cell type number could lead to a progressive pattern in the upper bound of extant cell type number, and really, it’s a kind of attempt at curve fitting to those fuzzy points. They come to the conclusion that about one new cell type emerges every 3 million years, and that extrapolating backward, the metazoa arose about 600 million years ago. They also want to argue that the Cambrian “explosion” did not involve any significant increase in complexity, contra Gould’s then-current thesis that would have predicted a sharper step function, rather than that steadily rising curve. Unfortunately, given the unassessed variability present in the data, I don’t see how they can decide that curve could be any better than just about any other.
Other serious problems in the data are that 1) it ignores life history information, and 2) consciously does not consider complexity in the nervous system! The first means that many of the invertebrate phyla, with their more elaborate temporal segregation of morphology, are going to have their cell types more seriously undercounted than are the vertebrates, and most of the groups before the 500 million year mark are going to have their complexity underestimated. The second problem is particularly serious for a paper that is trying to argue that there is no step function in the emergence of complexity—they are throwing out the most complex tissue type in the data. Even if their curve is real, they’re neglecting a large pedestal of complexity all across the board.
That’s a huge mistake. I’m fairly familiar with the insect neurodevelopment literature, so when I saw papers saying arthropods only have 50-60 cell types, alarm bells started ringing. My postdoc was spent staring at the nervous system of early embryonic grasshoppers, and I knew well all the membranes, the hemocytes, the tracheal epithelia, the various kinds of glia, the specialized midline tissues, the cuticle, the forming gut, the peripheral sensillae and supporting cells, muscles, fat, various glands, etc., without even considering the neurons…and with the neurons, oh boy. Here’s a diagram from the work of Chris Doe of a single side of a single developing ganglion, showing just the neuroblasts; not the neurons that will eventually arise from them, but just the progenitor cells that lie on the floor of the CNS. If you look at just the latest stage at the bottom right, there are about 30 different neuroblasts there, each with a unique identity. They all look pretty much the same, and I suspect that someone without much detailed knowledge would just say they’re all one neuroblast cell type, but the insect knows otherwise. The color-coding is used to indicate the combinatorial expression of a large subset of known molecules with differential expression. They may look the same, but at the level of what the genes are doing, they all have their own unique pattern.
I’m also familiar with some embryonic vertebrate nervous systems, and I can say that they tend to have many more cells in them — but they don’t seem to be as precisely identified at the single cell level as the invertebrate CNS. We have large populations of cells with similar patterns of molecular specification, rather than this kind of precise, cell-by-cell programmatic identity.
Now, from a genetic perspective, which pattern is more complex? I don’t know. They’re both complex but in very different ways—it’s basically impossible at this point to even identify a quantifiable metric that would tell us how complex either of these kinds of systems are. How many cell types are present in this whole animal? I don’t know that either. I’d want to look at a whole constellation of markers for their genetic regulatory state, a huge task that I haven’t seen done by anyone yet, and that would have been impossible in 1964, when Sneath made his estimates. I bet it’s many more than 60, though.
I’ll go out on a limb and make a prediction: any difference in the degree of complexity, assuming an objective method of measurement, in the triploblastic metazoa will much be less than an order of magnitude, and that the vertebrates will all be roughly equivalent…and that if any group within the vertebrates shows a significant increase in genetic complexity above the others, it will be the teleosts. I’ll also predict that any ‘extra’ complexity in members of these groups will not be a significant factor in their fitness, although it might contribute to evolvability.
The idea that complexity is a material and significant element in the genome, one that has a pattern of increase that has reached its pinnacle in humanity, is little more than one of the last vestiges of the mistaken notion of progress in evolution, and one that seems to be supported only by largely imaginary evidence. In particular, the often expressed idea that people, of all creatures, must be especially complex is like hearing someone with no knowledge of pianos explain that their favorite piano sonata is so wonderfully beautiful that it must have been played on an instrument with many more than 88 keys—and that Jerry Lee Lewis and Beethoven couldn’t possibly have been composing on similar instruments.
Bonner JT (1974) On Development(amzn/b&n/abe/pwll). Harvard, Cambridge.
Kauffman S (1995) At Home in the Universe(amzn/b&n/abe/pwll), Oxford University Press, New York.
Sneath PHA (1964) Comparative biochemical genetics in bacterial taxonomy. in Taxonomic biochemistry and serology, Leone CA, ed. Ronald, New York.
Valentine JW, Collins AG, Meyer CP (1994) Morphological Complexity Increase in Metazoans. Paleobiology 20(2):131-142.
Metamorphosis is a very complex process, one that seems to require the organisms that go through it to have very sophisticated and complicated genomes.
Why would anyone think that a human being is more complicated than a frog, on the level of molecular biology? It’s humans’ minds that are unusual, not the vast majority of our physiology.
But, but, but…humans are OBVIOUSLY more complex than flies. The creationist/IDers tell us so!
Seriously, having seen flies close up, they certainly don’t look obviously less complex than us. One look at their eyes is sufficient.
More importantly, if all life had a single ancestor, then every creature alive today is exactly as far removed in time from abiogenesis as all of us. People making ladder arguments talk about “lower” life forms like they just popped up from the past. In the case of those species with more rapid breeding and shorter life spans, they are FAR further removed from abiogenesis than we are in terms of generations, and therefore had more opportunity to evolve, so its not absurd to think they might be MORE complex than we are. The chimps are a great example.
Ah, we had arguments about this matter of “complexity” in my evolution class. I think the key problem is Linnean methods of classification, which almost seems to immediately set up the idea of the evolutionary ladder. Not to mention other phylogenetic issues, but I won’t go there.
this is why dawkins wrote The Ancestors Tale “backwards”
Great article, it’s one of those oddities of humanity that even as we continually show that we’re not special, we cling to our delusions of grandeur. When will we learn that being part of nature is infinitely better than being above it all?
(Shrug.) There’s really no reason to suppose we are more “complex” than flies, whales, or plants. However, I think its fairly self-evident that there has been an increase in complexity over time, and by “over time” I’m speaking about the period of time from the earth’s first organism to modern life. The first organism with replication molecules (probably RNA), likely had a small genome (as least in terms of RNA bases that were actually contributing to the organism’s survival – which is contrasted with useless RNA junk). After the organism started replicating, the “species” could begin to accumulate useful RNA sequences through natural selection. That “accumulation” was also an accumulation of complexity. When PZ Myers states:
I just think: “No, you’re wrong. There has been an increase in ‘complexity’. I think you’re going down a dead-end here.” I don’t necessarily think one modern organism can be categorized as “more complex” or “higher on the ladder” than another modern organism – at least not easily. However, I do think that evolution has increased the ‘complexity’ or ‘information’ of organisms over time by retaining past mutations and slowly adding new ones. Like I said, I think it’s fairly self-evident that the first life on earth was pretty simple; nothing like the complexity of modern multicellular organisms.
Great article, PZ. Left me more confused on the issue than I was to begin with. I think it’s an interesting question as to whether complexity has increased (in terms of the biosphere in general or the most complex organisms) both on Earth and in evolutionary systems in general. It’s too bad that question is so hard to define. There’s probably quite a bit to be learned from that observation too.
Excellent post.
Any graph with humans at the top is a big red flag for me. It’s not just the issue of species “complexity” either. Every other week there’s another book published identifying some general feature of our psychology as unique. Awareness, self-awareness, etc. It seems the more basic it is, the more it sets other animals apart from us as unconscious husks, the more likely someone is to identify it as the development that foreshadowed language and culture and other (supposedly) uniquely human attributes.
I think this is also one of the motivations for identifying every cultural practice as a sort of “proto-science.” Alchemy, astrology, religion. If everything is science then whatever development “sets us apart” from “the animals” had to be something big and profound and general because we’re “seekers of truth.” But if you look at history, science is a recent anomaly, and we don’t appear to have been much interested in truth. I think whatever developments made us “uniquely human” are much more specific, more niche, and less profound than some general “truth-seeking behaviour.” But we lucked out: in some tiny slice of human history, in some small portion of human culture, for their own idiosyncratic reasons (and read the writings of the time; they’re quite alien to us now), a handful of people chanced on the way of doing things we call science.
I think the phenomena of language and culture will turn out to be much less profound than most people assume. The problem is one of perspective: we find it very difficult to attribute mere animal behaviour to things we imbue with such value and meaning. It’s difficult to appreciate the phenomena from the inside looking out. But again to return to the current academic trend of seeing every cultural practice as a form of science: the reason we had institutions of alchemy, cosmogony, astrology, medicine, education, etc, long before we had anything substantive (or effectual) to organise such practices around is not because they were “proto-sciences” reflecting our innate desire for truth but because our current scientific institutions reflect existing human categorisations and practices of organisation. Medicine was a category long before we were capable of curing anything and modern medicine inherited those roots. Even our modern institutions of medicine and science and education are the products of a highly idiosyncratic species that happened upon the scientific method and not those of a species bent on understanding the Universe.
There’s no reason to think we need to be so special.
I recall reading a comment that may be relevant to all this. Someone pointed out that that ‘cold-blooded’ life needs more genes since each enzyme will work well over only a limited temperature range & eg: a lizard will need a few different enzymes for each needed reaction to allow it to function over the range of 0 °C to 50 °C, while a lion just needs one enzyme for each reaction since its body is always in a range of a few °C. So endothermy allowed a useful simplification of the genome.
I expect someone here can tell this non-biologist whether there is something very wrong with this idea.
Back a long time ago, maybe even high school long ago, I saw the comment, approximately, “We are told that life is in a steady progression from Paramecium to Philosopher. Unfortunately, though, it is the Philosopher that gives us this assurance.”
Very good essay, PZ.
What a wonderful post, a beautifully skeptical echo of Darwin’s reminder (in his notes) to avoid saying ‘higher’ or ‘lower’. Anyway, PZ, thanks, this one goes into the save file!
SH
I was going to make a comment very similar to tinyfrog’s first paragraph. I agree that complexity has obviously increased since the very first organsims.
However, tinyfrog goes a step too far in saying PZ is wrong. There’s a big difference between “evolution posits an increase in complexity” and “evolution posits a steady increase in complexity from bacteria to Homo sapiens.“
Re: Jim Baerg
I’m not aware of organisms having multiple enzymes to carry out the same function at different temperatures, though I’m not much more knowledgeable than you on this subject. However my impression is that most exotherms tend to live in a narrower temperature range than the 0 to 50C range you gave as an example, so endothermy would more useful to allow a greater range in habitat, rather than simplifying genomes.
I could see this idea as somewhat plausible. If I’m correct in that most endotherms don’t make use of redundent enzymes for different temperatures, it probably has to do with enzymes being partially functional even when it’s not under optimal conditions. It is probably more efficient to make use of less active enzyme than to synthesize different enzymes in different conditions.
I was recently at a “Body Worlds”-type exhibition. (You know, naked and plasticized humans that have been partially dissected and arranged artistically to illustrate the functions and interactions of various systems.) On a big sign as you first enter the display was a sign whose first statement was, “Humans are the most complex organisms ever to exist on Earth.” I sighed, perhaps a bit too loudly, and explained to my friends and everyone within listening distance just how equally complex many other organisms are. I think I annoyed the people working the exhibition. A little. But at least nobody was attributing anything to a nameless and formless diety.
Interesting post! And I agree: the ladder can be quite misleading.
*However*, what about say the complexity of life during the first billion years vs. the 2nd billion, 3rd billion (ok, I’m thinking big time scales here ;-)
Or more specifically, aren’t the Major Transitions in Evolution (e.g. a la Maynard Smith) evidence of an not all too surprising necessary increase in complexity, starting with the early days of life?
While the ladder (and the human at the top of it) can be very misleading, wouldn’t it also be misleading to not admit that there is a clear increase in complexity from very early life forms (e.g. prior to the emergence of cells) to those at a later stage (e.g. the emergence of life forms that study the songs of whales). There must be something going on there, mustn’t it?
Also can one put an estimate at when the “ramping up” phase has ended? When did the complexity curve (when suitably defined) start to flatten out?
Very interesting. We’re so used to thinking in heirarchies and organizing information according to perceived patterns. We find it difficult to admit those patterns might be partially or entirely of our own construction. That objective reality might in fact be very different.
Of course there were patterns of increasing complexity early in life’s history. I don’t know when or how quickly the transitions occurred. I do think a lot of the evolutionary changes that enabled multicellularity accumulated in single-celled organisms for a long time before they reached a threshold level — and maybe “threshold” is the magic word here. There are steps where a certain level of complexity is reached and then life spends a long period of time exploring and expanding within that complexity domain until another threshold is reached.
There could also be more steps to the process than we currently know about. Maybe all the clades that emerged out of the Cambrian radiation have roughly equal complexity levels, or maybe there are additional steps at, say, the agnatha, the ray-finned fishes, the tetrapods, the mammals. But the data aren’t convincing on any of it right now.
Hey PZ,
Nice discussion. But I’d like to point out some things.
1) the whole discussion of cell types (as you point out) is off
2) the number of genes is off
When I think of cell types I have in mind broad categories such as like neurons, sperm, GI track epithelial cells, muscle cells. Flies have these. Worms have ’em too. And in the end our gene counts are all in the same ballpark as well. As I’ve said before all of our studies in Cell Biology point to the fact that besides the housekeeping genes, most gene products are tools that all these cell types need. Any complexity/plasticity that one might ascribe to our brain’s development has more to do with when and where genetic programs are turned off or on regardless of whether you think our brain is or isn’t more complicated than a fly’s brain. I guess that’s the main point that I wanted to get across.
I don’t agree on that. I just don’t think that we really had a way of going beyond the means of knowledge that the Church Hierarchy allowed in order to start the exploration of truth in an objective manner. Revelation was accepted as a valid way of discerning truth up through the enlightenment, and has only been recently discarded when the scientific method showed that revelation has little value.
But, I take away from this post that as our scientists learn more and more about the way life works, we really have to shift our definition of complexity from the way it has been perceived up to this point.
I learned that it is not the number of genes that define complexity, but the means available for their expression of phenotypes is one way of defining complexity. I didn’t know that before.
Now, as to whether the harpsichords that Beethoven used to compose his music are similar to the pianos that Jerry Lee Lewis used; well I can only say this. Both were far more complex than whatever the hell John Tesh is using.
Another point. To deny that human behavior and cognitive ability is more complex then that of a fly is taking an argument to an extreme. It is a legitimate question as to why humans have the cognitive ability to speak, read, perform calculus etc. You might skate around the question by challenging that these phenotypes are not necessarily more complex than a flie’s ability to negotiating flight – but comm’on. You yourself admit that mechanisms that produce the human brain are probably more plastic and less deterministic then the brain development in flies, so you yourself attempt to explain this obvious difference between humans and flies! And you use Larry’s reason #5 on top of it!
S.J. Gould makes this point over and over in his essays: the “tree” or “ladder” is really a bush, and the typical organism on Earth is still single-cell. What’s happened is that the tail of the size-distribution has lengthened over time, though the modal value hasn’t moved.
I guess maybe creationists don’t read S.J. Gould so much, despite his church-hugging tendencies.
But to deny that these are the result of a more complex genome is not.
Science Avenger:
I think your idea of complexity might need some refinement there, too. Repitition of a similar structure doesn’t contribute to complexity much.
I think there’s another misleading way of thinking overlooked here, besides the matter of measuring “complexity”. The whole idea of counting “cell types” seems to me irredeemably hopeless. Categories and classifications can be wonderful things, properly used, but the cells in an organism just don’t give you much in the way of borders to split one group from another. About the only thing one could really say with certainty is that the number of types is greater than or equal to one (“type, human”), and it’s less than or equal to the number of cells in the organism.
If you try to be any more specific than that, I’d think you’d come up with a problem somewhat similar to the real numbers in math: any arrangement of groups you could come up with, I could make reasonable arguments why more of them are similar, and there should be fewer types, or why some of them you consider to be one type are somewhat different, and there should be more types. (Until you come up against one or the number of cells, of course.)
In short, the idea of “cell types” to be counted is just about as bogus as the “complexity” they’re trying to measure with it.
I was going to say “couldn’t agree more”, but I could.
It is true that complexity can be measured many different ways, but so far as I can figure out, there is only one way which has any relevance to evolution. That is “the amount of information which has a positive impact on selection”. Instead of droning on in this little box, I’ll just post a link to an JTheoBio article laying the idea out in detail:
http://arxiv.org/abs/quant-ph/0301075
In short, not only is that latter wrong, our intuitive notions of “information” and “complexity” are irrelevant (as well as being neigh impossible to actually measure). There is a relevant way to measure such things, but no one else seems to have noticed despite it being bloody obvious IMO.
BTW: About the “latter”… I just like pointing out that every extant species on Earth has evolved for the same amount of time. One can argue that bacteria (or insects if you must go multicellular) are even more highly evolved than mammals since most species have shorter generation times and are under stronger selection.
latter != ladder… damn I can’t spell ;)
This is true; however, one could argue that the neural system needed to transform the responses of that many lenses to photon frequency data into a usable “image” is a pretty powerful argument against the idea that arthropods are “less complex” than vertebrates, at least in that area. In fact, one group of arthropods, the stompatopods, arguably possesses the most complex visual system of any clade on earth.
PZ: Two questions…
First, if you had to pick a species or group to name as the “most evolved mammal” what would it be? (Inspired by my Human Evolutionary Biology teacher’s assertion that the aye-aye is the most “evolved” primate). More specifically, if you had to pick a group, which would you say represents the most dramatic departure from “typical” mammalian limb morphology (and is my intuition that sloths are pretty high on that list correct?).
Second, I think it might be helpful for clarifying for people like tinyfrog if you summarized your point here as an argument against claims of ranked differential genetic complexity, especially in a way that favors humans.
Can metrics for software complexity be ignored in any really meaningful penis-measuring contest in the context of the evolution of nervous systems?
Anyway, I wonder if this idea of humans necessarily having greater genetic or biological complexity, in its modern form, isn’t partly driven by some of the assumptions behind the “Marching Morons” thing you refuted a while ago, namely an inappropriate and fallacious assumption that behavioral and intellectual traits have a simple and direct correspondence to genetic attributes, coupled to the (accurate, as I understand it) observation that taken as a whole, human social behavior and analytical capacities are far more complex than those of any other animal species?
Apparently the library at your very own university owns a copy:
It’s even listed as “Not Checked Out” (though of course that doesn’t automatically equal “On the Shelf, Exactly Where It Should Be”). Even if it’s not to be found there for some reason (e.g., it was eaten by undergrads, etc.), if you’re truly curious about the chapter in question, no doubt the fine librarians there could get hold of a copy via interlibrary loan (WorldCat lists 462 copies in various libraries in the U.S.).
Is a bacterium simple or complex? If we consider a single bacterium in isolation, we can see it as very simple. But if we look at the biofilm inside your kitchen drain, we can simplify what we think we see by arbitrarily defining a few layers of films, then simpify further by arbitrarily mapping out zones within layers, always isolating this and that, in order to make us feel like we understand everything that is going on, but we’re only fooling ourselves. The complexity of a single biofilm is enough to make our heads hurt, if we let it.
Is water simple or complex? If we consider a single molecule, we can see it as very simple. But if we look at the ever-changing structure of even the thinnest film of water, it quickly becomes more complex than we can fathom.
“Why would anyone think that a human being is more complicated than a frog, on the level of molecular biology?”
I think the mammalian immune system is more sophisticated than that of an amphibian. But that doesn’t mean more genes are needed to specify it. The amphibian may well be more complicated.
A computer program written by a beginner will use many more lines of code than a program written by an expert which has all the same functions. The expert’s program will include general-purpose subroutines that can do various jobs depending on the arguments supplied to them. The beginner’s will have specific code for each job.
We need to distinguish between sophistication and complication.
Ah, but is the immune system really more complex in a mammal than a frog? A shorthand description of the immune system is that it is a relatively (important modifier, there) simple system that allows the generation of a great diversity of response elements. I’m going to say it again: I don’t know. We don’t have a useful, sharp, clear definition of organismal complexity.
Another analogy: Conway’s game of life. We start with very simple rules that allow for very complex instances of expression. Is it simple or complex? You’d rightly say that the rules are simple, but the patterns are complex, and those are two different aspects of the thing. Maybe biology is the same way. If we think of genes and gene interactions as rules analogous to Conway’s life, and the pattern of the organism in a species as an instantiation of the execution of a particular set of rules, then we can say that we’re both relatively simple and complex.
Conway’s life has 3 explicit rules, while we have on the order of 10,000±. I’m just saying that I think we and flies both have a core of equivalent complexity that is in excess of what we need to generate organismal complexity, so the whole argument about how we can explain our ‘deficiency’ of genes is misplaced.
The observation that there is no ladder is probably more damaging for creationists. It is also a remaining problem outside their ranks. But the ladder problem is really a subset of their ‘no change’ framing which doesn’t go away if the ladder does.
The observation that there is no ladder is probably more damaging for creationists. It is also a remaining problem outside their ranks. But the ladder problem is really a subset of their ‘no change’ framing which doesn’t go away if the ladder does.
Yes, the ladder is rubbish, but we have to be able to deal with the way in which humans deal with, organize and use information. We are the only species that uses bulldozers, flies planes, does quadratic equations and has advanced technology.
I think genetically this could be quite simple – but what is clearly happening is that on the level of information the humans acts as one or more large organism, sharing and storing data retrieving it from data banks and in other ways and also working cooperatively. Not many of our big successes have been the work of one person not building on what went before. The small switch that enabled this would appear to have to do with devolping an arbitrary symbolic language.
Those graphs look, in spirit and general character, an awful lot like the ones Ray Kurzweil used to promote the Technological Singularity.
In organisms, the “complexity” is not in the number of genes, or bits of DNA, but rather in the interaction between those bits of DNA and the products of those bits of DNA and the products of the products.
Complexity doesn’t scale as n, it scales as more like n!.
Complexity is not readily apparent or easily quantified. Hemoglogin is pretty well understood. A slight mutation (sickle cell trait) confers resistance to malaria. Which form of hemoglobin is the more complex?
But more complex doesn’t mean “better” even when “intelligently designed”. Which is more complex, Windows or Linux? Which is “more evolved”? Which is better? These value judgements require a “goal”. If the “goal”, is which OS will make Bill Gates more money, Windows wins hands down.
Careful with that “scales as n!” argument — that could be Larry’s Rationalization #8. It also doesn’t answer the question, because humans do not have the largest n.
But in principle, yes, that’s part of what I’m saying. Potential organismal complexity is an immense product of the number of genes, which is instantiated in a more limited expression in actual species. “n!” is huge, greater than we implement as a practical matter, so saying humans need “(n+1)!” is a pointless and undemonstrated exercise.
And why would ‘complexity’ be a desirable and superior trait in the first place?
Ever see a Rube Goldberg cartoon? Each design is a far more complex way of accomplishing a task than the generally-utilized methods, but I can’t think of anyone who would say that Goldbergian machines are better than the mundane ways.
Execellent! “there is no ladder”! I don’t know if your creationist readers are quite ready to build arguments on this new ground but it is the ground and some of us have our feet firmly upon it.
The ladder metphor begs us, among other things, to define which way is up. purely cultural judgements in a science question are a dead giveaway that the frame is wrong.
Thanks PZ!
That’s why this ole geologist hangs around here.
When the “junk DNA” term arrived I speculatively re-named it “toolbox”. Useful possibilities have been required before in every clade.
Every critter is an “intermediate form”.
the harpsichords that Beethoven used to compose his music
[pedantry]
Hmph. Beethoven knew how to play the harpsichord quite well (as do I), but he definitely composed for the piano. In fact, he was one of the musicians most responsible for early piano repertory and indeed for the development of the piano itself (he was much stronger, on the whole, than the poor delicate things, so he went through them like work shoes). What’s more, he probably composed a good deal of his piano music away from the piano, especially during that large part of his later career in which he was too deaf to even hear it.
[/pedantry]
Since I have nothing substantive to say about the science… lol.
Of course there are trend in evolution – some are passive (i.e., evolution away from starting minima due to increase in variance – e.g., start with one cell, you have no place to go but two or more) and some are active (i.e., driven by selection). Sean Carroll wrote an interesting perspective on this in 2001 – but some of his arguments are wrong, I think.
In the end, selection-driven evolutionary trends can lead towards increased complexity, decreased complexity, or comparable complexity. The way that you characterize the trend probably depends upon which of the characteristics that changed you are interested in.
Jim Valentine illustrates this point well with his discussions of a brick wall versus a pile of bricks. It takes more words to describe the detailed structure of a pile of bricks… are they more complex?
I think PZ may be misinterpreting Kauffman’s goal in counting cell-types. Kauffman was attempting to derive a relationship between the number of genetic switches, and the number of stable basins of attraction (which is to say cell types). He was not attempting to assign any particular direction to evolution.
No, I understood Kauffman’s work, and I even like it — it’s an interesting example of how complex properties may be specified by the nature of a network, independent of the details of the gene-by-gene interactions. That’s why I said it was excellent and thought-provoking. On the details of the biology, it falls flat. That graph was an example; another is regulatory rules he describes for his NK networks, which don’t correspond at all well with actual regulatory control in biological organisms.
I know he wasn’t arguing for teleology at all — his thesis is that islands of order are a natural consequence of the properties of the universe. In that section, though, he is trying to draw a correlation between genome size and complexity at the cellular level, and that doesn’t hold up at all well.
Stephen J. Gould on complexity and “the ladder” in 1994. Well, he gets to it eventually.
How about metabolic complexity? The bacterium Shewanella sp. for instance, can “breathe” iron, manganese, uranium, fumarate, nitrate, nitrite, arsenic and many other terminal electron acceptors, in addition to the oxygen that your fancy-pants eumetazoans can’t live without. Hell, you can’t even fix your own nitrogen!
It strikes me that ‘complexity’ is part of the human value system (like ‘beauty’ or ‘justice’). As such it is open to misinterpretation because of cultural biases.
Unless we can define complexity in such a way that machines or aliens could could use, and agree the results with us, the debate is sterile. Much like the way Dr Dembski snuck human values into design detection through his idea of Complex Specified Information.
On alternative splicing:
When I interviewed at Harvard for grad school a few years back, I met with a guy that studied a particular gene in Drosophila- I think it was a neuronal transmembrane/signaling protein. (I wish I could remember the name of the guy or the protein.) This gene in Drosophila was alternatively spliced in well over a hundred different ways. He speculated that it was involved in specific cell/cell recognition and wiring, but no one really knew. Anyway, the same gene is not alternatively spliced in mammals. That’s just one example, but I doubt that there’s more alternative splicing in mammals versus insects.
On genome size/gene number:
There are some simple organisms with such beautiful streamlined little genomes. Aren’t there even viruses that have overlapping ORFs for different genes? How can you not call that “highly evolved?”
Also, I’ve heard the argument that some species have large genomes with lots of padding because they need big cells with big nuclei. (The reverse of this argument was used to argue that dinosaurs had small genomes, because they had small cells.)
Finally, there are some plant species that have huge genomes because they speciated by polyploidy. Is a new polyploid species suddenly twice as complex?
On transposons:
Come on, these were discovered in plants. Also, I don’t think that having a genome littered with the corpses of ancient parasites (LINE and SINE elements) makes one more complex. It’s actually sort of scary, if you think about how much of our genome is made up of these things.
If you’re just talking about the placental + marsupial clade (Theria), 130 million sounds good. If you mean all mammals (any evidence that monotremes have fewer cell types? … Didn’t think so), you reach something like 170 or 180 million years.
And… you know better than to say “the invertebrate CNS”!
You should read Gould’s book Full House. Life happens to have started near the lower end of the possible range of complexity; the range occupied by life has increased, but the vast majority of life has more or less stayed where it was, there are more movements downwards than upwards, and the upper end reached by life seems not to have moved for the last, say, 450 million years at the very least.
It’s the range of complexity that has increased, not the complexity.
Not the tetrapods in any way I can think of. (If anything, the loss of the median fins and the gill lids should be counted as a couple of simplifications.)
I don’t know if that’s libel or slander… only tenured professors take stuff from university libraries and never give it back!
Mind the gray parrots.
Some have amazing cases of that.
That puts the complexity on the insect side, however. A unique gene expression pattern for every single neuroblast is awesome.
If you’re just talking about the placental + marsupial clade (Theria), 130 million sounds good. If you mean all mammals (any evidence that monotremes have fewer cell types? … Didn’t think so), you reach something like 170 or 180 million years.
And… you know better than to say “the invertebrate CNS”!
You should read Gould’s book Full House. Life happens to have started near the lower end of the possible range of complexity; the range occupied by life has increased, but the vast majority of life has more or less stayed where it was, there are more movements downwards than upwards, and the upper end reached by life seems not to have moved for the last, say, 450 million years at the very least.
It’s the range of complexity that has increased, not the complexity.
Not the tetrapods in any way I can think of. (If anything, the loss of the median fins and the gill lids should be counted as a couple of simplifications.)
I don’t know if that’s libel or slander… only tenured professors take stuff from university libraries and never give it back!
Mind the gray parrots.
Some have amazing cases of that.
That puts the complexity on the insect side, however. A unique gene expression pattern for every single neuroblast is awesome.
Another point of comparison on complexity vs. simplicity: To use a computer programming example, look what you have to go through to get the smallest and, probably, simplest executable possible on an ELF/Linux system. The process to produce it is rather complex, including overlapping different header areas that are read from different starting points, which reminds me very much of some of the tricks genes can play. So, is it simpler or more complex than a standard program that functions the same? All depends on how you look at it.
Steevl hits the nail on the head!
In addition, why compare humans to flies if you are talking about language and calculus? What you need to do (as PZ and others pointed out) is find increased complexity in the human genome compared to chimps and other mammals. Good luck with that.
By the way, why isn’t anyone arguing that there must be increased complexity in the honey bee genome compared to other insects? The complex society! The dance language! And yet they have less genes than fruit flies – what an affront!
Beautiful post, PZ.
This issue of complexity ‘arising’ out of evolution, as if that was amongst its essential mechanistic features, has long since become chronically entrenched. Everybody reflexively speaks of evolution running from “simple molecules” towards “complex organisms”, so it would probably take a major paradigm shift to dislodge the erroneous aspect of the notion that suggests a driving force or at least some kind of essential characteristic aspect driving evolution. No upheaval, necessarily, but perhaps a new perspective might serve.
The fitting into potential niche environments emerging from the co-evolution of biological communities (including the specialization of cells within multi-cellular organisms) cannot help but lead to an increase in the elaboration of adaptive traits. Genomic fine-tuning of individual organisms or species aside, I seriously wonder whether the “complexity” issue isn’t something that ought more accurately or meaningfully be directed at the information content of whole ecologies, or even the entire biosphere (that is, as SYSTEMS), rather than constantly aiming the focus of attention towards individual species or their genetic content.
No organism – none of us – can be defined solely on the basis of our genes. Might it not be that a significant part of the complexity issue is misdirected: that the fundamental selection mechanisms as they impinge on genetic complexity is not the same as the information content at the much larger scales and contingincies of interaction and behavior based on the phenotypic expression of those genes?
Just a suggestion, but it seems to me that any attempts at comparitive complexity within genes is rather as impotent as determining relative complexity of computer software codes: the implied correlation between complexity and genes badly misses the mark.
The informational complexity is in the expression, and we ought to remember that very simple codes can lead to very complex functions, while extremely complex codes can yield garbage. The cumulative nature of selection will build up a stock of whatever works, any complexity at the level of genetic codes notwithstanding.
I just wonder if information theory wouldn’t have a more relevant bearing on the elaboration of system complexity. Assuming stable or suitable planetary environments, couldn’t we expect THIS kind of informational complexity with time to be an ubiquitous feature wherever life gains a foothold in the universe?
Wanda, I think you might be thinking of Dietmar Schmuker at Harvard who has been working on alternative splicing of Dscam and how the molecular diversity in Dscam leads to wiring patterns between sensory neurons and their targets (all in drosophila). His group has published a few amazing papers in the last year in Cell and Neuron on the topic. Alternative splicing of Dscam can lead to up to 38,016 different receptors!
The primary argument of ID’ers is that complexity (or complex systems) cannot be generated through a series of random events. But aren’t chaotic systems themselves extremely complex? Could they be define as infinitely complex? Can a series of random events within an infinitely complex system lend itself to the formation of life as we know it?
Anything made by a human is defined (by ID’ers) as ‘intelligently designed’ and therefore, not the result of random events. But isn’t it thought that most brain activity is due to the random firing of neurons? It would appear that random neuronal activity _can_ design intelligently.
Mike Haubrich: But note that in many respects Christendom was a reversal – Aristotle and Socrates, Thales and Epicurus would have refused arguments from revelation.
Interestingly, I just came across this passage in a book I’m reading right now called A Natural History of the Sonoran Desert:
I bet that line throws some readers for a loop. I wonder if they might consider toads some of the “highest life forms” in this context because of their control over respiration when they bury themselves in the mud?
Great discussion! Reading this post and all the comments makes me wonder if complexity is in fact an ontological property or just an epistemological one. Is complexity an attribute of things or is it an attribute of knowledge, of how we see and understand things?
I would guess that among tetrapods, birds are the most different from a basal ancestor. Thus they are the most highly evolved. But complexity? There I’d supspect that all tetrapods and even vertebrates are on the same level. And of course bony fishes (teleosts) win the prize for greatest number of different species.
It makes sense that most metazoans are at more or less the same order of complexity.
Clarification: I should have said that among vertebrates, teleosts have the most species. I do remember that “the Almighty had an inordinate fondness for beetles.”