Saturday, July 31, 2010

Watching the evolution knobs spin

Evolution really happens at the dials controlling genes, more than in protein sequences those genes encode.

The shock of humans having only ~23,000 genes has yet to fully sink in. Fewer genes than soybeans? Than the potato? Additionally, the depth to which some of these genes are conserved is also astonishing, with a promoter of eye development working quite well when transplanted into fruit flies. What, then, makes us different? What has evolution been doing all this time?

A recent paper in science adds evidence that far more variation goes on in the promoters of genes than in their coding sequences. The authors tracked the sites of action (i.e. DNA binding) of two liver-specific transcription regulatory proteins in chickens, opossum, mice, dogs, and humans, and found that few  were recognizably conserved. Most sites disappeared, reappeared, altered, and mutated with considerable abandon.

The regulators themselves (CEBPA, and HNF4A) were very well conserved, meaning that as proteins, they had virtually the same sequence in each organism. And more critically, their preferred binding site on DNA stayed the same as well. That tends to be hard to change if their binding to thousands of different sites (~20,000 is the estimate given for each protein) is important for an organism's liver and other organs. Putting it in technical terms, such binding specificities tend to be subject to strong purifying selection.

On the other hand, the individual sites are much less constrained by evolution, since changes affect only that individual target gene. Some genes that have been studied as targets of CEBPA include metabolic enzymes, detoxifying enzymes like cytochromes P450, EPHX1, and SULT2A1, several insulin-regulated genes, growth factors, the gene for albumin, coagulation factor VIII, and other transcriptional regulators in liver development and function.

The current authors use some high-tech wizardry to isolate all the DNA bound to these regulatory proteins from each species of interest, and sequence around each site to see where it maps in the respective species' genome. This gives them the dataset of sites that they then mine to ask whether the sites have stayed consistent over evolutionary time. The answer is no: "For these two liver-specific TFs, binding events appear to be shared 10 to 22% of the time between mammals from any two of the three placental lineages we profiled, separated by approximately 80 million years of evolution (figs. S6 and S7). This result reveals a rapid rate of evolution in transcriptional regulation among closely related vertebrates."

For example, they show the binding of CEBPA to one region around the gene for PCK in liver. Phosphoenolpyruvate carboxykinase is a metabolic enzyme which helps synthesize glucose.

The coding exons of the PCK1 gene are shown at the lower right. kb = kilo basepairs. Hsap = human, Mmus= mouse, Cfam = dog, Mdom = short tailed opossum, and Ggal = chicken.

The pattern in chicken is quite simple. More sites appear in the mammals, with novel and significant sites appearing in dogs and humans. The scoring of these sites is somewhat unclear, in terms of how minor a site could be and still score, not to mention that they had no functional tests of which sites actually affected local gene transcription.

A key and well-occupied site right at the start of the PKC1 gene is well-conserved, however, and probably has a dominant regulatory role. What role the other sites might have is not clear, and might be minimal. So their  conclusion needs to be taken with a bit of salt, as they indicate that most of the highly conserved DNA binding sites are at this kind of most-influential position near genes that rely heavily on regulation by the bound regulator.

Nevertheless, the reason for flexibility in regulator binding is not hard to find, since binding sites are often composed of only six or eight nucleotides, with sloppy allowances for binding to sites with some mutations as well. New sites can appear easily, and old sites can be destroyed just as easily. So these regulatory proteins bind all over the genome and these sites change frequently, allowing regulatory variation to happen easily by mutation. The authors conclude "Taken together, the steady accumulation of small changes in the genetic sequence appears to rapidly remodel thousands of TF binding sites in mammals." [TF refers to transcription factor, another word for DNA binding regulator].

Given the complexity of biology, the network is the real locus of evolution, with the pieces (proteins encoded by genes) being shuffled around by regulatory experiments over time. Indeed, another recent paper compared the multicellular organism Volvox with its single-celled relative Chlamydomonas, and found that they had almost exactly the same number of genes, and few gene differences overall. They conclude: "This is consistent with previous observations indicating co-option of ancestral genes into new developmental processes without changes in copy number or function." And one of the most important mechanisms of such co-option is placing the given gene under novel regulation. This process is slightly reminiscent of the human economy, which is being driven increasingly as a "knowledge economy", shuffling around financing, software, and organization while the basic commodities of existence remain far more constant.

  • Free will, explained. (Only in part, however.. it leaves out our moral responsiveness to others.)
  • A judicious analysis of the wikileaks doc dump.
  • The Taliban is getting desperate and may be in decline.
  • MMT economics in a nutshell.
  • Walter Mead pens an uncharacteristically idiotic screed against the greens. As if "prohibition" were being proposed by anyone, anywhere. Note the mash note to fellow anti-green Andrew Revkin.
  • Meanwhile, yet another CO2 related apocalypse rears its head.
  • Bill Mitchell quote of the week, speaking of Minsky's model of financial cycles, requiring broad anti-cyclical policy as well as (right now) government stimulus:
"Through phases of recession, recovery, tranquility, and euphoria, the economy endogenously moves from robust to fragile financial structures. The fragile structure characterised by high levels of speculative and Ponzi finance becomes vulnerable to a multitude of shocks, any of which, in isolation or concert, can alter perceptions of future income flows needed to validate the debt structure and drive the economy into crisis."

Friday, July 23, 2010

Mind of matter

I propose a tentative model of qualia and consciousness.

A rich thread of comments over at another blog motivated me to tackle the problem of consciousness with as much specificity as evidence currently allows, including the voluminous evidence for its material basis. So here I try to lay out a plausible model of fully brain-based consciousness, to address the dualist, who typically says that he or she can not imagine any material basis to consciousness, and even claims that there is some kind of philosophical necessity that the "hard problem" of consciousness is beyond scientific analysis entirely. (I have previously written about the neurobiology of consciousness, which remains unresolved.)

As a philosophical naturalist, I would predict that no new physics will be required to resolve the consciousness problem (such as 5th dimensions, quantum consciousness in microtubules, etc.). It is pretty clear that the brain is a messy product of evolution and works by electrochemical / molecular mechanisms. It is encoded by DNA, bounded by physical space (the head), and is affected at all levels by known lesions, chemicals and other effects. Nothing more esoteric is likely to show up in its study, other than incredibly intricate organization, which we still have great difficulty analyzing as a purely technical matter.

That leaves us with either an identity position that dualists don't seem to understand, (that there exists some brain-based processes that are objective physical events and also constitute subjective consciousness at the same time), or an eliminativist position, which we all dislike (that consciousness doesn't really exist). The problem may go away, but surely not by claiming that we have no consciousness after all. Indeed, the fact that there are unconscious processes that include forms of perception, intuition, and many other computations means that there is some real distinction between things that are unconscious and those that enter consciousness, and thus that consciousness is not an epiphenomenon or semantic issue.

So I should explain the identity position a bit better, despite the admitted lack of a real scientific solution in place.

Everyone has heard about continuity in movies- the need to keep hairstyles constant, props in the same places, etc. even when a shoot of one scene goes over several days, so that the illusion of continuity is preserved. I think this is a big clue to consciousness, which could be thought of as consisting, in part, of a brief memory loop that keeps our experience continuous. The ability to associate a split-second ago with now gives us not only a sense of time, but of consciousness itself, since otherwise we would be bombarded by what seem random stimuli, uncontrolled, uncorrelated, and meaningless.

So that is part of the answer, which can be easily imagined to be embodied by the gamma wave system in the brain that is the humming in-phase communication of ever-changing coalitions of neurons from all over. This would be the perfect system to glue together percepts and mental contents while giving them limited continuity of a fraction of a second, some of which is then stored to short-term memory, which is so notoriously poor, (hippocampus), some of which is stored in turn to longer-term memory (frontal cortex). Recalling something from memory weakly re-creates the engram (gamma pattern) that was originally driven by the perceptual system, and engages the same consciousness system, though with much lower intensity and different feel. We need a prompt like a smell or madelaine to assemble the engram again more fully, though it is never again quite the same as the first time in any case.

But we still have not gotten to the heart of the issue- the redness of red. We know that lesions like strokes can cancel out perceptions very selectively. There was a recent New Yorker article on the inability to read words while having unimpaired vision- an amazingly specific stroke effect. But the funny thing is that the sufferers routinely have to deduce their deficits. If something is missing, even something like half the visual field, we are not notified. The consciousness system soldiers on as though nothing has happened, forming an impression of the world that feels complete out of all the remaining bits and pieces.

Thus consciousness is very grade-able, both among humans with various talents and deficits, and among animals with different senses and brain sizes, as well as within one person in different moods, states of sleep, Dilbertian meetings, etc. It is also the kind of system that presents whatever comes up and doesn't care about what is missing. This again fits the gamma wave system, which wouldn't join up nerves that were not firing, but would just assemble whatever forms a minimal coalition of activity. And lastly, I'll make a stop at synesthesia, where one sensory modality bleeds into another, for instance inducing people to perceive certain numbers as having particular colors wherever they appear. The cause seems to be a literal mixing of neurons in relevant areas of the brain, which has obvious selective implications, both for problems arising from extensive wrong-wiring, and for the possible creativity and special perceptual powers that might result from limited cross-wiring.

What is red? Remember that red is a complete fabrication- our brain's way of mapping qualia to what in physics are numerically different wavelengths of light. The brain can apparently make anything it likes of the stimuli coming in. We should not be surprised if bats see their sonar world in living color as well. The question is why red feels so immediate, and what transaction actually occurs between red and "our perception" of it. In other words, what is the difference between unconscious and conscious information processing?

The difference seems to lie in entry into a privileged process in the brain, such as perhaps the gamma wave system. Other areas of the brain may talk to each other and process information, but that does not enter consciousness. Whatever does enter consciousness comes from relatively high level areas of processing, by virtue of the brain's wiring, which mostly flows from inputs (signals from the eye) to higher levels of processing that are biased towards participating in these gamma wave coalitions (analyses of shape, object identity, face identity, motion, etc.). Some people such as artists may able to "see" a scene without a lot of computational processing and overlaid interpretation, but as it is at a more basic sensory level, implying that they have conscious access to unusual levels of processing.

So consciousness is a part of a unique level of processing, where interpretations are collected and cross-correlated and learned from. Why does that feel real as unconscious processing clearly does not? Incidentally, unconscious processing may be just as complex, as we learn from our social intuitions, which can be incredibly spot-on and discerning about situations we have given little conscious thought to. Dreams also point to enormous depth and richness to unconscious processes, so it may be a mistake to put all this in some kind of higher/lower hierarchy.

A sense of reality may in this theory be the product of pure associational power- the construction of a sufficiently complex and rapidly integrated virtual world becomes what we call consciousness. If everything we see instantly generates a map of spatial, social, artistic, analytical, and other associations, that alone gives the scene "reality", immediacy, and red-ness. Seeing red becomes conscious not through some magical or impossibly recurrent homunculus behind our eyes, but by its particularity in contrast to other sensations and its web of immediate associations with the vast arrays of implicit and explicit knowledge we carry around in the database of our heads.

Suppose you were to see a uniform field of red all the time, day in and day out. You would no longer be conscious of red at all. You would not only be seeing the world through rose-colored glasses, but be seeing only the rose colored glasses and nothing else. Had you no other senses, you would probably lose consciousness altogether, a sensory-deprived victim of extreme torture. But of course we have many other senses- sound, smell, touch, and several newly discovered ones, such as body and spatial sense and the like. We also have dreams- the ability to draw on our voluminous past sensory impressions and their plastic re-arrangements in imagination. So it is literally impossible to do this kind of experiment.

This theory can account for the graded-ness of consciousness, its natural development through evolution, its materiality, and in addition provides a program for the instantiation of such experiences in artificial systems. It informs the common observation that high-level consciousness is dependent on knowledge, such that the study of art history gives us new eyes in museums, and the study of biology gives us new eyes in nature. It also provides a program for the study of consciousness, since its physical correlate should be quite discrete and find-able (by the identity theory mentioned above). It is in the correlation of subjective consciousness to this postulated physical correlate that the test will be found, either confirming detailed correspondence, and driving other theories to extinction, or not.

Lastly is the issue of emotion and pain. The above theory deals with cognitive consciousness, like *appreciating what red is in an immediate way. Emotions are simpler, not necessarily association-based. They are prior to high-level cognition. Past pain is certainly a strong spur to current aversion by association, but how did past pain happen? How was it perceived? There is something elemental and not associative about raw emotions like pain, which form perhaps our first and most traumatic form of consciousness.

Pain can function without consciousness at all. We typically notice that we have pulled our hand from the fire after the deed is done, and wonder at the reflex. But pain can also flood consciousness, issuing its imperative command to fix whatever is wrong. Similarly, other emotions typically operate below consciousness, to the point that our partners are often more familiar with our tics, mannerisms, and broadcast emotions than we ourselves are. As above, the cognitive contents of emotions can be characterized as associative, (what hurts, who did it to us, what is causing pleasure, etc.), but emotions carry extra contents injected alongside as the valence of the pleasure or pain- the command by other systems of the brain that this is something to be done again, or never again.

So it is no surprise that consciousness seems to be a complicated system, requiring rapid and  wide-spread associations to provide the brute contents and textured differentiation of cognition, as well as a brief memory loop that gives continuity to experience. Emotions are injected as extra cognitive contents and feelings, using specially responsive brain areas that date from early evolution and provide more than information: motivation.

I have tried to present a model that is plausible given current evidence, though obviously not very detailed. While there is plenty of circumstantial evidence that something material and eletrochemical in the brain is responsible, it will take a few decades yet to fill in those details.

  • Theologians working at public universities find it getting hot under the collar.
  • Can you lose your sense of smell
  • A billion dollars here, a billion dollars there...
  • One gets the impression that Hamid Karzai doesn't know much about power.
  • Though his isn't the only government beset with unaccountable bloat and corruption.
  • An interesting reflection on the worth of work:
".. while collecting salaries of between £500,000 and £10 million, leading City bankers destroy £7 of social value for every pound in value they generate." ... ".. for every £1 they are paid, childcare workers generate between £7 and £9.50 worth of benefits to society."

Saturday, July 17, 2010

Go, LeBron!

LeBron James knows what business he's in.

Sorry to stray from my usual dour topics, but the recent LeBron James saga has thrown some interesting light on labor in America. Commentators have been piling on about his narcissism, his breathtaking gall, his callous rending of Cleveland's heart, and the botched PR that will see him rot in hell. Or something like that.

Topping it all was the Cavalier's owner, who threw a titanic snit at losing James to Miami and apparently learning about it on TV along with the rest of us. To which I say, tough luck!

James put the NBA owners through their paces, subjecting them to the most abject groveling, before arranging a prime time extravaganza to burn his bridges to all but one. Where else have we seen a powerful and energetic black man, sometimes referred to as "the one", calling the shots? Firing generals? Showing the man who's boss? Being the man?

So let us not cry for the NBA owners, with their anti-trust exemption. Through their ministrations, the NBA has far more teams than talent. Way too many games are scheduled and as a result, injuries are rampant. The game has become relentlessly physical and combative under NBA refereeing. In Cleveland, James was expected to carry the team mostly by himself, and was unable to make it work. In desperation, they imported Shaquille O'Neal, creating a situation more comical than effective. James did the rational thing and created a better situation for himself elsewhere. All NBA teams try to nurture and milk home-town sentiments ... until they don't, trading players as though they were slaves on the auction block. It was nice to see the tables turned for a change, frankly.

The way I see it, James's primary motivation was to play with his friends and fellow stars, Wade and Bosh. And these are very honorable motives. The US army relies first and foremost on comraderie to build units that fight effectively. This seems lost on the modern NBA, where players are shuffled around on the basis of little more than management hunches, statistics, and needed positions. My local team, the Warriors, has seen season after season end up high in the draft due to terrible chemistry, starting from its top management. One player went so far as to physically choke the coach. Thankfully, both are retired now and resting peacefully. Conversely, the Boston Celtics assembled a star threesome several years ago of Paul Pierce, Ray Allan, and Kevin Garnett, which worked on the levels of both chemistry and talent, to ensuing acclaim. Few thought that Garnett should have slaved on in Minnesota to the end of his career.

In this way star players are taking control of their careers, and in turn, of the league, typically not to make more money, but to play with colleagues they like, and thence to be successful on premier teams- teams that the NBA is structured by its owners to avoid, based on its collusive drafting and salary cap rules. The owner-player tension is evident, and we shouldn't mind the ball going into the player's basket every so often through canny self-promotion and sheer talent.

Lastly, why do it on TV? Wasn't that shockingly self-aggrandizing? Well, the high ratings speak for themselves. If nine million people watch, then it is by definition not self-aggrandizing, it is entertainment, which is, after all, the business the NBA is in. To which, I say, well done, LeBron!

Saturday, July 10, 2010

Kant and the cognitive bootstrapping problem

It turns out that our brains come pre-patterned to deal with space, time, causality, language, and morality, among other a priori concepts. Where did they get them? From evolution, of course.

Respect for dead philosophers is an odd thing. They are often revered for introducing ambitious systems of esoteric metaphysics. Occasionally for having novel ideas. Sometimes they even write well. The questions they raise are perennial and to some, fascinating. But rarely have they solved anything. Ambitious systems are propounded in one era only to be forgotten or overturned in the next, at best remembered by a catchphrase, like "God is dead", or "thesis, antithesis, synthesis". It may be a brutal disservice to the history of ideas to encapsulate the multi-volume cogitations of past philosophers in such token fashion. But unless they have supplied solutions to some of the perplexities of existence, what else can we in all honesty do?

Immanuel Kant grappled with our capacity to reason, among much else. He realized (as prodded by Hume) that experience alone was not enough, combined with reason, to organize our thoughts about the world. We need to have some pre-existing template into which to pour all those experiences, like a basic grid of space, time, and a sense of causality, if we are to have any hope of getting off the ground. Which is to say- our minds can not be an empty slates if we want to learn anything. Or to put it another way, we can not epistemically pull ourselves up by our own bootstraps. Thus he came up with a priori concepts, which he took to be given structures of the mind, however the mind comes to be.

From the wiki pages: "... Kant is thought to argue that our representation of space and time as a priori intuitions entails that space and time are transcendentally ideal." ... "According to Kant, a priori knowledge is transcendental, or based on the form of all possible experience, while a posteriori knowledge is empirical, based on the content of experience." ... "Something is transcendental if it plays a role in the way in which the mind "constitutes" objects and makes it possible for us to experience them as objects in the first place."

Despite Kant's other ventures in defense of god and of free will, this aspect of his ideas did not neccessitate any opinion on how the structure of our minds arises, and is thus quite consistent with modern cognitive psychology and developmental psychology.

Two recent papers deal with development of spatial consciousness in rats. Incidentally, another recent paper shows that this system (spatial representation and memory across the entorhinal cortex and hippocampus) which is so well studied in rodents, works the same way in humans, studied by way of strokes that create transient dead spots in the hippocampus. The rat papers study very young rats, just as their eyes have opened and they have their first exploratory experience outside the nest, to tell whether their hippocampal and entorhinal place memory/sensing systems are already in place, or only form later after further experience. Their conclusions agree that, while experience helps this system grow both physiologically and in behavioral accuracy, it is in place from the earliest times.

The hippocampus is the location for storing temporary memories, and also for place memory. It is telling that a popular memorization trick among the ancients was to vizualize a palace with endless rooms, where arbitrary memories are stowed by location, available for retrieval later. In the contemporary world, graphical metaphors lead the way in computer user interfaces, giving us "windows" on virtual spaces that organize our affairs far more richly and naturally than text indexes, file trees, or other more easily-implemented methods.

The hippocampus gets its location input from the entorhinal cortex, which is in turn connected to the inner ear, vision, and other sensory systems. The entorhinal cortex contains neurons that respond to head orientation, spatial grid at various scales, borders, and absolute location. This means that scientists have been able to record the activities of neurons that fire only when the rat faces a particular direction relative to its environment, or crosses an imaginary line in an arbitrary polygonal grid that divides up its environment, nears a spatial border, or hits a particular location or landmark.

These cells are assumed to be directly involved in the animal's consciousness of place, since their removal dramatically impairs their ability to learn mazes and know where they are. The question then is... when is all this information set up? We know that learning creates new grids, landmarks, and borders all the time. But is there anything in this system at the start, as neurons get wired up? These papers claim that yes, there is.

They inserted electrodes into the relevant location of 16 day-old rat pups, and found that already at this time, two days after their eyes have opened, and before significant mobility, they have head direction cells and place cells, and one paper finds grid cells as well at this early time.

Example from Langston, et al. showing the location of probes in the entorhinal cortex (A), and local neural firing rates (with peak firing frequency noted) of presumptive head-direction cell recordings, plotted vs actual head direction (B).

Unfortunately, for all the technical pain of doing this kind of work on such young animals (for all concerned!), I don't think they did this early enough. Even with their eyes closed, infant rats are probably acutely aware of place, if only to find the mother's nipple. Vision is not the only input to the entorhinal cortex, so doing this work soon after the eyes open seems insufficient to say that the overall space orientation system is in some part natively present by genetically-driven development alone. Indeed, even in the womb, babies probably have some notion of space, since they are kicking around and active.

As Langston et al. conclude, "Whether the formation of prototypical representations in the parahippocampal and hippocampal cortices requires translational or vestibular experience at younger ages, in the next, remains to be determined."

So the ideal experiment would seem virtually impossible to do- to isolate a developing rat's entorhinal cortex (and thus hippocampus) from external influence to see what the brain wires up all by itself. This could be done by severing the inputs in such a way that they could not regrow. Which would probably derange its development substantially, by cutting off the nerves invading from the sensory areas. Would that tell us that modest inputs from very early times may have strong influences on the nascent wiring? The hard part would be to measure the naive neuronal maps- if they have no input, then how can we measure them? How can a grid cell fire if the rat can't detect a grid? At that point, we might have to resort to dreams as a way of probing the native capabilities of the brain. Could a rat with no spatial experience or sensation still have spatial dreams? Now that would be an interesting question!

In the end, this work seems at best indicative of the conclusions they claim. I would generally agree that the Kantian a priori concepts of space and much else are pre-wired in the brain in some way, based in turn on the evolutionary patrimony of embodied knowledge gained through the school of hard knocks. But the very concept of brain "wiring" is transgressive, both carrying information and constituting information derived from past development and genetic influences. Mammalian fetuses experience things from some early point in time, based to various degrees on genetic wiring. From there on, development is a mad dash of experience and genetic patterning each feeding off the other to generate that mighty device- the fully formed brain.

I realize that this work does not even try to address the a priori concepts of morality, time (also here), social relations, language, etc. I believe they follow the same pattern of modest pre-patterning combined with intertwined experiential development, which the interested reader may wish to study.

  • Corruption rampant in the oil industry, with taxpayers on the hook.
  • Why macroeconomics is different from regular economics.
  • Skidelsky dismantles Osborne.
  • On the internet, no one knows you're a stutterer. That is, until you podcast!
  • Tom Tomorrow draws a few crocodile tears.
  • Enlightenement, shmenlightenment, Texas style.
  • The media likes to be "balanced", except when it doesn't.
  • Bill Mitchell quote of the week: He advocates that the government directly employ excess (unemployed) labor at a sustainable minimum wage, rather than acceding to the business practice of casting them out onto the street.
"Given the overwhelming central bank focus on price stability, and the critical role of today’s buffer stocks of unemployed, we argue that functioning and effectiveness of the buffer stock is critical to its function as a price anchor.
Condition and liquidity are the keys. Just as soggy rotting wool is useless in a wool price stabilisation scheme, labour resources should be nurtured as human capital constitutes the essential investment in future growth and prosperity. There is overwhelming evidence that long-term unemployment generates costs far in excess of the lost output that is sacrificed every day the economy is away from full employment.
It is clear that the more employable are the unemployed the better the price anchor will function. The government has the power to ensure a high quality price anchor is in place and that continuous involvement in paid-work provides returns in the form of improved physical and mental health, more stable labour market behaviour, reduced burdens on the criminal justice system, more coherent family histories and useful output, if well managed."

Saturday, July 3, 2010

Apocalypse now

Biodiversity is going downward fast. What are we going to do about it?

Now that the climate change policy is limping forward again after some media outlets retracted their criminally lazy and uninformed coverage far too late to do anyone any good. Now that international scientific work of the IPCC has been validated and cleared all over again in all its essentials ... perhaps we can get down to where we should have been a decade ago- addressing our fossil carbon addiction and its planet-wide perils.

Another international consortium got together (pursuant to a 2002 Convention on Biological Diversity) to publish a paper on the state of worldwide biodiversity, and the news is not good. Human pressure on environments is going up, biodiversity is going down, and human conservation responses, though significant, are not sufficient to alter the trend. Here is the summary figure:

The state (of biodiversity) graph may not seem so terrible, with declines in our lifetimes (since 1970) of about 18% in aggregate over all the dimensions (many studies, over 5,000 populations) the group measures. But zero on this graph is really zero- no biodiversity. One species: humans. That is not a happy thought to contemplate. I can not really comment on their other axes, but their aim is to present trends happening over the last forty years as holistically and globally as possible. 

For one component ....
"The index was calculated using time-series data on 7190 populations of 2301 species of mammal, bird, reptile, amphibian and fish from around the globe."

One would have to note that the effect of humans on the environment hardly started forty years ago, either. Many of the most famous extinctions happened long before, such as the Dodo, the passenger pigeon, Stellar's sea cow, and on back to the extraordinary megafauna of pre-human North America.

Here are some more detailed components that are worrisome:

For me, biodiversity is the core issue with climate change and all the other harms we are doing to the biosphere. If the sea rises and cities are swamped, we can move and rebuild. But when species go extinct, that is pretty much forever. With DNA technology we may eventually be able to bring species back in some form, but what, frankly, would be the point? Without rich ecosystems, they would be just as stranded as before. Whether the atmosphere and rocks heat up is of no concern. But the fate of life on the planet- that is of great concern.

The root cause of this decline is obviously human overpopulation multiplied by economic development, integrated over lack of insight, foresight, and moral responsibility. Our powers as humans have become vast, and unexpectedly we have come up against ecological limits and harms that tax our powers of conception. That is why scientists have been in the lead sounding the alarm bells- they both love nature intensely, and have the capacity and tools to conceive of what is going on. 

But no one individually can divert this train to tragedy. We have to take collective action to avert collective disaster. What we do collectively is a moral question- do we sacrifice today (carbon tax, larger wild land reserves, a ban on ocean fishing, birth control) so that we and future humans (not to mention other creatures) can exist in a more harmonious and beautiful world?

Indeed, just to give an idea of the scale of the current downturn, this is the overall employment level since 1950, courtesy of BLS:

There have been pauses in employment growth over this time, but never the kind of course reversal we saw over the last few years. Note that this data is more informative than "unemployment", which ignores anyone discouraged enough to not be looking for work, and many other questionable corrections. And here is a ratio of employment to population. Note that the current level has declined to near the 1950's to 1970's levels, when the proportion of women employed was much lower than today.